diff --git a/data/a4base/bioconda_a4base.yaml b/data/a4base/bioconda_a4base.yaml index 4e9fa49016ce1..769bacf8fb943 100644 --- a/data/a4base/bioconda_a4base.yaml +++ b/data/a4base/bioconda_a4base.yaml @@ -3,7 +3,6 @@ description: Automated Affymetrix Array Analysis home: https://bioconductor.org/packages/3.10/bioc/html/a4Base.html identifiers: - biotools:a4base -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-a4base diff --git a/data/a4core/bioconda_a4core.yaml b/data/a4core/bioconda_a4core.yaml index 7d0fd069569c4..1334e26a78163 100644 --- a/data/a4core/bioconda_a4core.yaml +++ b/data/a4core/bioconda_a4core.yaml @@ -3,7 +3,6 @@ description: Automated Affymetrix Array Analysis Core Package home: https://bioconductor.org/packages/3.10/bioc/html/a4Core.html identifiers: - biotools:a4core -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-a4core diff --git a/data/a4preproc/bioconda_a4preproc.yaml b/data/a4preproc/bioconda_a4preproc.yaml index 891c52b9135bb..87e91acf85f16 100644 --- a/data/a4preproc/bioconda_a4preproc.yaml +++ b/data/a4preproc/bioconda_a4preproc.yaml @@ -3,7 +3,6 @@ description: Automated Affymetrix Array Analysis Preprocessing Package home: https://bioconductor.org/packages/3.10/bioc/html/a4Preproc.html identifiers: - biotools:a4preproc -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-a4preproc diff --git a/data/a4reporting/bioconda_a4reporting.yaml b/data/a4reporting/bioconda_a4reporting.yaml index 825aec23cd814..cc00205c7675f 100644 --- a/data/a4reporting/bioconda_a4reporting.yaml +++ b/data/a4reporting/bioconda_a4reporting.yaml @@ -3,7 +3,6 @@ description: Automated Affymetrix Array Analysis Reporting Package home: https://bioconductor.org/packages/3.10/bioc/html/a4Reporting.html identifiers: - biotools:a4reporting -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-a4reporting diff --git a/data/affycompatible/bioconda_affycompatible.yaml b/data/affycompatible/bioconda_affycompatible.yaml index b629f83b7643b..4ccf459f14684 100644 --- a/data/affycompatible/bioconda_affycompatible.yaml +++ b/data/affycompatible/bioconda_affycompatible.yaml @@ -7,7 +7,6 @@ description: This package provides an interface to Affymetrix chip annotation an home: https://bioconductor.org/packages/3.10/bioc/html/AffyCompatible.html identifiers: - biotools:affycompatible -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-affycompatible summary: Affymetrix GeneChip software compatibility diff --git a/data/affycontam/bioconda_affycontam.yaml b/data/affycontam/bioconda_affycontam.yaml index 08534c2bf6e97..ff97652ed225d 100644 --- a/data/affycontam/bioconda_affycontam.yaml +++ b/data/affycontam/bioconda_affycontam.yaml @@ -3,7 +3,6 @@ description: structured corruption of cel file data to demonstrate QA effectiven home: https://bioconductor.org/packages/3.10/bioc/html/affyContam.html identifiers: - biotools:affycontam -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-affycontam summary: structured corruption of affymetrix cel file data diff --git a/data/affycoretools/bioconda_affycoretools.yaml b/data/affycoretools/bioconda_affycoretools.yaml index a9283951af825..b43c17a7dde42 100644 --- a/data/affycoretools/bioconda_affycoretools.yaml +++ b/data/affycoretools/bioconda_affycoretools.yaml @@ -4,7 +4,6 @@ description: Various wrapper functions that have been written to streamline the home: https://bioconductor.org/packages/3.10/bioc/html/affycoretools.html identifiers: - biotools:affycoretools -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-affycoretools summary: Functions useful for those doing repetitive analyses with Affymetrix GeneChips diff --git a/data/affyexpress/bioconda_affyexpress.yaml b/data/affyexpress/bioconda_affyexpress.yaml index cc1060e852d48..aef2fc7724e26 100644 --- a/data/affyexpress/bioconda_affyexpress.yaml +++ b/data/affyexpress/bioconda_affyexpress.yaml @@ -5,7 +5,6 @@ description: The purpose of this package is to provide a comprehensive and easy- home: https://bioconductor.org/packages/3.10/bioc/html/AffyExpress.html identifiers: - biotools:affyexpress -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-affyexpress diff --git a/data/affyio/bioconda_affyio.yaml b/data/affyio/bioconda_affyio.yaml index 5aebe4b2fb86e..8a9749e5f2121 100644 --- a/data/affyio/bioconda_affyio.yaml +++ b/data/affyio/bioconda_affyio.yaml @@ -4,7 +4,6 @@ description: Routines for parsing Affymetrix data files based upon file format i home: https://bioconductor.org/packages/3.10/bioc/html/affyio.html identifiers: - biotools:affyio -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-affyio diff --git a/data/annaffy/bioconda_annaffy.yaml b/data/annaffy/bioconda_annaffy.yaml index ef2b403fbcebf..4097a325a60c1 100644 --- a/data/annaffy/bioconda_annaffy.yaml +++ b/data/annaffy/bioconda_annaffy.yaml @@ -6,7 +6,6 @@ description: Functions for handling data from Bioconductor Affymetrix annotation home: https://bioconductor.org/packages/3.10/bioc/html/annaffy.html identifiers: - biotools:annaffy -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-annaffy diff --git a/data/annotate/bioconda_annotate.yaml b/data/annotate/bioconda_annotate.yaml index 4275538c580be..3f050c1e66cd8 100644 --- a/data/annotate/bioconda_annotate.yaml +++ b/data/annotate/bioconda_annotate.yaml @@ -3,7 +3,6 @@ description: Using R enviroments for annotation. home: https://bioconductor.org/packages/3.10/bioc/html/annotate.html identifiers: - biotools:annotate -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotate summary: Annotation for microarrays diff --git a/data/annotationdbi/bioconda_annotationdbi.yaml b/data/annotationdbi/bioconda_annotationdbi.yaml index e695a0a3cd54f..836b879a72602 100644 --- a/data/annotationdbi/bioconda_annotationdbi.yaml +++ b/data/annotationdbi/bioconda_annotationdbi.yaml @@ -4,7 +4,6 @@ description: Implements a user-friendly interface for querying SQLite-based anno home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationDbi.html identifiers: - biotools:annotationdbi -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotationdbi summary: Manipulation of SQLite-based annotations in Bioconductor diff --git a/data/annotationforge/bioconda_annotationforge.yaml b/data/annotationforge/bioconda_annotationforge.yaml index f3fa58c27243c..5a8d9f6d09148 100644 --- a/data/annotationforge/bioconda_annotationforge.yaml +++ b/data/annotationforge/bioconda_annotationforge.yaml @@ -4,7 +4,6 @@ description: Provides code for generating Annotation packages and their database home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationForge.html identifiers: - biotools:annotationforge -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotationforge summary: Tools for building SQLite-based annotation data packages diff --git a/data/annotationfuncs/bioconda_annotationfuncs.yaml b/data/annotationfuncs/bioconda_annotationfuncs.yaml index ab46c6eca27d6..fa18d91c52787 100644 --- a/data/annotationfuncs/bioconda_annotationfuncs.yaml +++ b/data/annotationfuncs/bioconda_annotationfuncs.yaml @@ -4,7 +4,6 @@ description: Functions for handling translating between different identifieres u home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationFuncs.html identifiers: - biotools:annotationfuncs -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-annotationfuncs diff --git a/data/annotationhub/bioconda_annotationhub.yaml b/data/annotationhub/bioconda_annotationhub.yaml index 56213aec16adb..1ae3d1ec9edd4 100644 --- a/data/annotationhub/bioconda_annotationhub.yaml +++ b/data/annotationhub/bioconda_annotationhub.yaml @@ -9,7 +9,6 @@ description: This package provides a client for the Bioconductor AnnotationHub w home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationHub.html identifiers: - biotools:annotationhub -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotationhub summary: Client to access AnnotationHub resources diff --git a/data/annotationhubdata/bioconda_annotationhubdata.yaml b/data/annotationhubdata/bioconda_annotationhubdata.yaml index f1d2d27b71f1a..8e8f23ac5d611 100644 --- a/data/annotationhubdata/bioconda_annotationhubdata.yaml +++ b/data/annotationhubdata/bioconda_annotationhubdata.yaml @@ -4,7 +4,6 @@ description: These recipes convert a wide variety and a growing number of public home: https://bioconductor.org/packages/3.10/bioc/html/AnnotationHubData.html identifiers: - biotools:annotationhubdata -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-annotationhubdata summary: Transform public data resources into Bioconductor Data Structures diff --git a/data/arraytools/bioconda_arraytools.yaml b/data/arraytools/bioconda_arraytools.yaml index e4ce18b9e0f71..3e4eacd67f1fb 100644 --- a/data/arraytools/bioconda_arraytools.yaml +++ b/data/arraytools/bioconda_arraytools.yaml @@ -9,7 +9,6 @@ description: This package is designed to provide solutions for quality assessmen home: https://bioconductor.org/packages/3.10/bioc/html/ArrayTools.html identifiers: - biotools:arraytools -- doi:10.1038/nmeth.3252 license: LGPL (>= 2.0) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-arraytools diff --git a/data/aspli/bioconda_aspli.yaml b/data/aspli/bioconda_aspli.yaml index bcbfc3d7600b5..e64b21095fcc7 100644 --- a/data/aspli/bioconda_aspli.yaml +++ b/data/aspli/bioconda_aspli.yaml @@ -3,7 +3,6 @@ description: Integrative pipeline for the analysis of alternative splicing using home: https://bioconductor.org/packages/3.10/bioc/html/ASpli.html identifiers: - biotools:aspli -- doi:10.1038/nmeth.3252 license: GPL license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-aspli diff --git a/data/bader/bioconda_bader.yaml b/data/bader/bioconda_bader.yaml index 722b13670258e..e1fb996a19c75 100644 --- a/data/bader/bioconda_bader.yaml +++ b/data/bader/bioconda_bader.yaml @@ -7,7 +7,6 @@ description: For RNA sequencing count data, BADER fits a Bayesian hierarchical m home: https://bioconductor.org/packages/3.10/bioc/html/BADER.html identifiers: - biotools:bader -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-bader diff --git a/data/badregionfinder/bioconda_badregionfinder.yaml b/data/badregionfinder/bioconda_badregionfinder.yaml index 0669a39c4d15b..c78e5763c66fc 100644 --- a/data/badregionfinder/bioconda_badregionfinder.yaml +++ b/data/badregionfinder/bioconda_badregionfinder.yaml @@ -6,7 +6,6 @@ description: BadRegionFinder is a package for identifying regions with a bad, ac home: https://bioconductor.org/packages/3.10/bioc/html/BadRegionFinder.html identifiers: - biotools:badregionfinder -- doi:10.1038/nmeth.3252 license: LGPL-3 license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-badregionfinder diff --git a/data/bamsignals/bioconda_bamsignals.yaml b/data/bamsignals/bioconda_bamsignals.yaml index af114fdcc2737..5f11655d8144a 100644 --- a/data/bamsignals/bioconda_bamsignals.yaml +++ b/data/bamsignals/bioconda_bamsignals.yaml @@ -5,7 +5,6 @@ description: This package allows to efficiently obtain count vectors from indexe home: https://bioconductor.org/packages/3.10/bioc/html/bamsignals.html identifiers: - biotools:bamsignals -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-bamsignals diff --git a/data/basespacer/bioconda_basespacer.yaml b/data/basespacer/bioconda_basespacer.yaml index 3565dc04f86e3..2ab7b0dd9b53d 100644 --- a/data/basespacer/bioconda_basespacer.yaml +++ b/data/basespacer/bioconda_basespacer.yaml @@ -4,7 +4,6 @@ description: A rich R interface to Illumina's BaseSpace cloud computing environm home: https://bioconductor.org/packages/3.10/bioc/html/BaseSpaceR.html identifiers: - biotools:basespacer -- doi:10.1038/nmeth.3252 license: Apache License 2.0 name: bioconductor-basespacer summary: R SDK for BaseSpace RESTful API diff --git a/data/beat/bioconda_beat.yaml b/data/beat/bioconda_beat.yaml index 542fb1a092787..a4f9b4f1d2ab8 100644 --- a/data/beat/bioconda_beat.yaml +++ b/data/beat/bioconda_beat.yaml @@ -3,7 +3,6 @@ description: Model-based analysis of single-cell methylation data home: https://bioconductor.org/packages/3.10/bioc/html/BEAT.html identifiers: - biotools:beat -- doi:10.1038/nmeth.3252 license: LGPL (>= 3.0) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-beat diff --git a/data/bgafun/bioconda_bgafun.yaml b/data/bgafun/bioconda_bgafun.yaml index 153cdc37a9835..7ebb68f8f3c0a 100644 --- a/data/bgafun/bioconda_bgafun.yaml +++ b/data/bgafun/bioconda_bgafun.yaml @@ -4,7 +4,6 @@ description: A method to identify specifity determining residues in protein fami home: https://bioconductor.org/packages/3.10/bioc/html/bgafun.html identifiers: - biotools:bgafun -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-bgafun summary: BGAfun A method to identify specifity determining residues in protein families diff --git a/data/bicare/bioconda_bicare.yaml b/data/bicare/bioconda_bicare.yaml index f3fa713eeeb43..878d2b00330a5 100644 --- a/data/bicare/bioconda_bicare.yaml +++ b/data/bicare/bioconda_bicare.yaml @@ -3,7 +3,6 @@ description: Biclustering Analysis and Results Exploration home: https://bioconductor.org/packages/3.10/bioc/html/BicARE.html identifiers: - biotools:bicare -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-bicare diff --git a/data/biocgraph/bioconda_biocgraph.yaml b/data/biocgraph/bioconda_biocgraph.yaml index 446c67fe0d470..14c23c9f49926 100644 --- a/data/biocgraph/bioconda_biocgraph.yaml +++ b/data/biocgraph/bioconda_biocgraph.yaml @@ -4,7 +4,6 @@ description: This package provides examples and code that make use of the differ home: https://bioconductor.org/packages/3.10/bioc/html/biocGraph.html identifiers: - biotools:biocgraph -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-biocgraph summary: Graph examples and use cases in Bioinformatics diff --git a/data/biocstyle/bioconda_biocstyle.yaml b/data/biocstyle/bioconda_biocstyle.yaml index 137b8a431fec5..48dad0e532fc5 100644 --- a/data/biocstyle/bioconda_biocstyle.yaml +++ b/data/biocstyle/bioconda_biocstyle.yaml @@ -4,7 +4,6 @@ description: Provides standard formatting styles for Bioconductor PDF and HTML d home: https://bioconductor.org/packages/3.10/bioc/html/BiocStyle.html identifiers: - biotools:biocstyle -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-biocstyle summary: Standard styles for vignettes and other Bioconductor documents diff --git a/data/biocviews/bioconda_biocviews.yaml b/data/biocviews/bioconda_biocviews.yaml index 82bb212d45ee6..0eddf9ef766fb 100644 --- a/data/biocviews/bioconda_biocviews.yaml +++ b/data/biocviews/bioconda_biocviews.yaml @@ -6,7 +6,6 @@ description: Infrastructure to support 'views' used to classify Bioconductor pac home: https://bioconductor.org/packages/3.10/bioc/html/biocViews.html identifiers: - biotools:biocviews -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-biocviews summary: Categorized views of R package repositories diff --git a/data/biodist/bioconda_biodist.yaml b/data/biodist/bioconda_biodist.yaml index bc4a9ae4f995d..7b49d570acc7e 100644 --- a/data/biodist/bioconda_biodist.yaml +++ b/data/biodist/bioconda_biodist.yaml @@ -3,7 +3,6 @@ description: A collection of software tools for calculating distance measures. home: https://bioconductor.org/packages/3.10/bioc/html/bioDist.html identifiers: - biotools:biodist -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-biodist summary: Different distance measures diff --git a/data/biomformat/bioconda_biomformat.yaml b/data/biomformat/bioconda_biomformat.yaml index 3cf5555b217f4..c331b55eb87ee 100644 --- a/data/biomformat/bioconda_biomformat.yaml +++ b/data/biomformat/bioconda_biomformat.yaml @@ -10,7 +10,6 @@ description: This is an R package for interfacing with the BIOM format. This pac home: https://bioconductor.org/packages/3.10/bioc/html/biomformat.html identifiers: - biotools:biomformat -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-biomformat diff --git a/data/biomvcclass/bioconda_biomvcclass.yaml b/data/biomvcclass/bioconda_biomvcclass.yaml index fe5e70023fc79..257b3ddd07c6a 100644 --- a/data/biomvcclass/bioconda_biomvcclass.yaml +++ b/data/biomvcclass/bioconda_biomvcclass.yaml @@ -3,7 +3,6 @@ description: Creates classes used in model-view-controller (MVC) design home: https://bioconductor.org/packages/3.10/bioc/html/BioMVCClass.html identifiers: - biotools:biomvcclass -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-biomvcclass diff --git a/data/biostrings/bioconda_biostrings.yaml b/data/biostrings/bioconda_biostrings.yaml index 80f6cf60cb050..9bb90c23c4e89 100644 --- a/data/biostrings/bioconda_biostrings.yaml +++ b/data/biostrings/bioconda_biostrings.yaml @@ -4,7 +4,6 @@ description: Memory efficient string containers, string matching algorithms, and home: https://bioconductor.org/packages/3.10/bioc/html/Biostrings.html identifiers: - biotools:biostrings -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-biostrings summary: Efficient manipulation of biological strings diff --git a/data/biosvd/bioconda_biosvd.yaml b/data/biosvd/bioconda_biosvd.yaml index d86ab677cda01..45906f5e50373 100644 --- a/data/biosvd/bioconda_biosvd.yaml +++ b/data/biosvd/bioconda_biosvd.yaml @@ -21,7 +21,6 @@ description: The biosvd package contains functions to reduce the input data set home: https://bioconductor.org/packages/3.10/bioc/html/biosvd.html identifiers: - biotools:biosvd -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-biosvd summary: Package for high-throughput data processing, outlier detection, noise removal diff --git a/data/biovizbase/bioconda_biovizbase.yaml b/data/biovizbase/bioconda_biovizbase.yaml index 5bf691c6544ca..31a2bf5c4ca83 100644 --- a/data/biovizbase/bioconda_biovizbase.yaml +++ b/data/biovizbase/bioconda_biovizbase.yaml @@ -6,7 +6,6 @@ description: The biovizBase package is designed to provide a set of utilities, c home: https://bioconductor.org/packages/3.10/bioc/html/biovizBase.html identifiers: - biotools:biovizbase -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-biovizbase summary: Basic graphic utilities for visualization of genomic data. diff --git a/data/blima/bioconda_blima.yaml b/data/blima/bioconda_blima.yaml index 66a36d09597b6..4acb19abcf944 100644 --- a/data/blima/bioconda_blima.yaml +++ b/data/blima/bioconda_blima.yaml @@ -10,7 +10,6 @@ description: Package blima includes several algorithms for the preprocessing of home: https://bioconductor.org/packages/3.10/bioc/html/blima.html identifiers: - biotools:blima -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-blima diff --git a/data/bsgenome/bioconda_bsgenome.yaml b/data/bsgenome/bioconda_bsgenome.yaml index 35f85d436d885..2a7877bdcc1c3 100644 --- a/data/bsgenome/bioconda_bsgenome.yaml +++ b/data/bsgenome/bioconda_bsgenome.yaml @@ -3,7 +3,6 @@ description: Infrastructure shared by all the Biostrings-based genome data packa home: https://bioconductor.org/packages/3.10/bioc/html/BSgenome.html identifiers: - biotools:bsgenome -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-bsgenome summary: Software infrastructure for efficient representation of full genomes and diff --git a/data/bufferedmatrix/bioconda_bufferedmatrix.yaml b/data/bufferedmatrix/bioconda_bufferedmatrix.yaml index c1bb59901ee2f..eb5869f28850a 100644 --- a/data/bufferedmatrix/bioconda_bufferedmatrix.yaml +++ b/data/bufferedmatrix/bioconda_bufferedmatrix.yaml @@ -4,7 +4,6 @@ description: A tabular style data object where most data is stored outside main home: https://bioconductor.org/packages/3.10/bioc/html/BufferedMatrix.html identifiers: - biotools:bufferedmatrix -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-bufferedmatrix diff --git a/data/bufferedmatrixmethods/bioconda_bufferedmatrixmethods.yaml b/data/bufferedmatrixmethods/bioconda_bufferedmatrixmethods.yaml index 69ce4ccd1267b..822220246e37c 100644 --- a/data/bufferedmatrixmethods/bioconda_bufferedmatrixmethods.yaml +++ b/data/bufferedmatrixmethods/bioconda_bufferedmatrixmethods.yaml @@ -3,7 +3,6 @@ description: Microarray analysis methods that use BufferedMatrix objects home: https://bioconductor.org/packages/3.10/bioc/html/BufferedMatrixMethods.html identifiers: - biotools:bufferedmatrixmethods -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-bufferedmatrixmethods diff --git a/data/bus/bioconda_bus.yaml b/data/bus/bioconda_bus.yaml index a4394c01d4bc1..369b0bf01c18d 100644 --- a/data/bus/bioconda_bus.yaml +++ b/data/bus/bioconda_bus.yaml @@ -4,7 +4,6 @@ description: This package can be used to compute associations among genes (gene- home: https://bioconductor.org/packages/3.10/bioc/html/BUS.html identifiers: - biotools:bus -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-bus diff --git a/data/cancerinsilico/bioconda_cancerinsilico.yaml b/data/cancerinsilico/bioconda_cancerinsilico.yaml index cc99b45b2ca8d..adc78d53e51a1 100644 --- a/data/cancerinsilico/bioconda_cancerinsilico.yaml +++ b/data/cancerinsilico/bioconda_cancerinsilico.yaml @@ -6,7 +6,6 @@ description: The CancerInSilico package provides an R interface for running math home: https://bioconductor.org/packages/3.10/bioc/html/CancerInSilico.html identifiers: - biotools:cancerinsilico -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-cancerinsilico diff --git a/data/cancersubtypes/bioconda_cancersubtypes.yaml b/data/cancersubtypes/bioconda_cancersubtypes.yaml index 6e742e386e9f0..d2aaeec892c28 100644 --- a/data/cancersubtypes/bioconda_cancersubtypes.yaml +++ b/data/cancersubtypes/bioconda_cancersubtypes.yaml @@ -6,7 +6,6 @@ description: CancerSubtypes integrates the current common computational biology home: https://bioconductor.org/packages/3.10/bioc/html/CancerSubtypes.html identifiers: - biotools:cancersubtypes -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-cancersubtypes diff --git a/data/category/bioconda_category.yaml b/data/category/bioconda_category.yaml index 3b926110dedf0..e396ed5568051 100644 --- a/data/category/bioconda_category.yaml +++ b/data/category/bioconda_category.yaml @@ -3,7 +3,6 @@ description: A collection of tools for performing category (gene set enrichment) home: https://bioconductor.org/packages/3.10/bioc/html/Category.html identifiers: - biotools:category -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-category summary: Category Analysis diff --git a/data/causalr/bioconda_causalr.yaml b/data/causalr/bioconda_causalr.yaml index 69eaa11119d0f..ec2a0f08545a4 100644 --- a/data/causalr/bioconda_causalr.yaml +++ b/data/causalr/bioconda_causalr.yaml @@ -4,7 +4,6 @@ description: Causal network analysis methods for regulator prediction and networ home: https://bioconductor.org/packages/3.10/bioc/html/CausalR.html identifiers: - biotools:causalr -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-causalr diff --git a/data/cellgrowth/bioconda_cellgrowth.yaml b/data/cellgrowth/bioconda_cellgrowth.yaml index 83d2ae0eda6da..6a80bd6809769 100644 --- a/data/cellgrowth/bioconda_cellgrowth.yaml +++ b/data/cellgrowth/bioconda_cellgrowth.yaml @@ -4,7 +4,6 @@ description: This package provides functionalities for the fitting of cell popul home: https://bioconductor.org/packages/3.10/bioc/html/cellGrowth.html identifiers: - biotools:cellgrowth -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-cellgrowth summary: Fitting cell population growth models diff --git a/data/chipseq/bioconda_chipseq.yaml b/data/chipseq/bioconda_chipseq.yaml index c568c10937e08..a98eb7585e16e 100644 --- a/data/chipseq/bioconda_chipseq.yaml +++ b/data/chipseq/bioconda_chipseq.yaml @@ -3,7 +3,6 @@ description: Tools for helping process short read data for chipseq experiments home: https://bioconductor.org/packages/3.10/bioc/html/chipseq.html identifiers: - biotools:chipseq -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-chipseq summary: 'chipseq: A package for analyzing chipseq data' diff --git a/data/chipsim/bioconda_chipsim.yaml b/data/chipsim/bioconda_chipsim.yaml index e8e2ca0795511..7c3a01c807e01 100644 --- a/data/chipsim/bioconda_chipsim.yaml +++ b/data/chipsim/bioconda_chipsim.yaml @@ -5,7 +5,6 @@ description: A general framework for the simulation of ChIP-seq data. Although c home: https://bioconductor.org/packages/3.10/bioc/html/ChIPsim.html identifiers: - biotools:chipsim -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-chipsim diff --git a/data/chopsticks/bioconda_chopsticks.yaml b/data/chopsticks/bioconda_chopsticks.yaml index 339c219303ecb..c4dc8beaa1ace 100644 --- a/data/chopsticks/bioconda_chopsticks.yaml +++ b/data/chopsticks/bioconda_chopsticks.yaml @@ -3,7 +3,6 @@ description: Implements classes and methods for large-scale SNP association stud home: https://bioconductor.org/packages/3.10/bioc/html/chopsticks.html identifiers: - biotools:chopsticks -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-chopsticks diff --git a/data/chromheatmap/bioconda_chromheatmap.yaml b/data/chromheatmap/bioconda_chromheatmap.yaml index 614321d356a7f..bcc151bb219c2 100644 --- a/data/chromheatmap/bioconda_chromheatmap.yaml +++ b/data/chromheatmap/bioconda_chromheatmap.yaml @@ -5,7 +5,6 @@ description: The ChromHeatMap package can be used to plot genome-wide data (e.g. home: https://bioconductor.org/packages/3.10/bioc/html/ChromHeatMap.html identifiers: - biotools:chromheatmap -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-chromheatmap summary: Heat map plotting by genome coordinate diff --git a/data/cindex/bioconda_cindex.yaml b/data/cindex/bioconda_cindex.yaml index e26d74b2db98b..27fafe20bfc2c 100644 --- a/data/cindex/bioconda_cindex.yaml +++ b/data/cindex/bioconda_cindex.yaml @@ -10,7 +10,6 @@ description: The CINdex package addresses important area of high-throughput geno home: https://bioconductor.org/packages/3.10/bioc/html/CINdex.html identifiers: - biotools:cindex -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-cindex diff --git a/data/cleaver/bioconda_cleaver.yaml b/data/cleaver/bioconda_cleaver.yaml index 6dead78bf7674..b0a9b1eb93e0b 100644 --- a/data/cleaver/bioconda_cleaver.yaml +++ b/data/cleaver/bioconda_cleaver.yaml @@ -4,7 +4,6 @@ description: 'In-silico cleavage of polypeptide sequences. The cleavage rules ar home: https://bioconductor.org/packages/3.10/bioc/html/cleaver.html identifiers: - biotools:cleaver -- doi:10.1038/nmeth.3252 license: GPL (>= 3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-cleaver diff --git a/data/clst/bioconda_clst.yaml b/data/clst/bioconda_clst.yaml index 77a8169846517..51605eb834423 100644 --- a/data/clst/bioconda_clst.yaml +++ b/data/clst/bioconda_clst.yaml @@ -4,7 +4,6 @@ description: Package for modified nearest-neighbor classification based on calcu home: https://bioconductor.org/packages/3.10/bioc/html/clst.html identifiers: - biotools:clst -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-clst diff --git a/data/clstutils/bioconda_clstutils.yaml b/data/clstutils/bioconda_clstutils.yaml index 07871e44e99b0..7db48c4d5aa6f 100644 --- a/data/clstutils/bioconda_clstutils.yaml +++ b/data/clstutils/bioconda_clstutils.yaml @@ -4,7 +4,6 @@ description: Tools for performing taxonomic assignment based on phylogeny using home: https://bioconductor.org/packages/3.10/bioc/html/clstutils.html identifiers: - biotools:clstutils -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-clstutils diff --git a/data/clustcomp/bioconda_clustcomp.yaml b/data/clustcomp/bioconda_clustcomp.yaml index e56fe03a16ce8..2b891e7a69796 100644 --- a/data/clustcomp/bioconda_clustcomp.yaml +++ b/data/clustcomp/bioconda_clustcomp.yaml @@ -16,7 +16,6 @@ description: clustComp is a package that implements several techniques for the c home: https://bioconductor.org/packages/3.10/bioc/html/clustComp.html identifiers: - biotools:clustcomp -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-clustcomp diff --git a/data/clustersignificance/bioconda_clustersignificance.yaml b/data/clustersignificance/bioconda_clustersignificance.yaml index 01886a21a1c4d..4d3e24383efc5 100644 --- a/data/clustersignificance/bioconda_clustersignificance.yaml +++ b/data/clustersignificance/bioconda_clustersignificance.yaml @@ -11,7 +11,6 @@ description: The ClusterSignificance package provides tools to assess if class c home: https://bioconductor.org/packages/3.10/bioc/html/ClusterSignificance.html identifiers: - biotools:clustersignificance -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-clustersignificance diff --git a/data/clusterstab/bioconda_clusterstab.yaml b/data/clusterstab/bioconda_clusterstab.yaml index b2dbe95ebae61..4ff0ae81d483a 100644 --- a/data/clusterstab/bioconda_clusterstab.yaml +++ b/data/clusterstab/bioconda_clusterstab.yaml @@ -4,7 +4,6 @@ description: This package can be used to estimate the number of clusters in a se home: https://bioconductor.org/packages/3.10/bioc/html/clusterStab.html identifiers: - biotools:clusterstab -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-clusterstab summary: Compute cluster stability scores for microarray data diff --git a/data/cner/bioconda_cner.yaml b/data/cner/bioconda_cner.yaml index d6e2400377ee3..1d3b766d4e2fc 100644 --- a/data/cner/bioconda_cner.yaml +++ b/data/cner/bioconda_cner.yaml @@ -4,7 +4,6 @@ description: Large-scale identification and advanced visualization of sets of co home: https://bioconductor.org/packages/3.10/bioc/html/CNEr.html identifiers: - biotools:cner -- doi:10.1038/nmeth.3252 license: GPL-2 | file LICENSE license_file: LICENSE name: bioconductor-cner diff --git a/data/cntools/bioconda_cntools.yaml b/data/cntools/bioconda_cntools.yaml index f38864fdc03e6..18fada4140a1f 100644 --- a/data/cntools/bioconda_cntools.yaml +++ b/data/cntools/bioconda_cntools.yaml @@ -5,7 +5,6 @@ description: This package provides tools to convert the output of segmentation a home: https://bioconductor.org/packages/3.10/bioc/html/CNTools.html identifiers: - biotools:cntools -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-cntools diff --git a/data/cnvgsa/bioconda_cnvgsa.yaml b/data/cnvgsa/bioconda_cnvgsa.yaml index 774dcac3edd76..aa936181314ef 100644 --- a/data/cnvgsa/bioconda_cnvgsa.yaml +++ b/data/cnvgsa/bioconda_cnvgsa.yaml @@ -4,7 +4,6 @@ description: This package is intended to facilitate gene-set association with ra home: https://bioconductor.org/packages/3.10/bioc/html/cnvGSA.html identifiers: - biotools:cnvgsa -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-cnvgsa diff --git a/data/cnvpanelizer/bioconda_cnvpanelizer.yaml b/data/cnvpanelizer/bioconda_cnvpanelizer.yaml index 6957386b24497..658d65d35676c 100644 --- a/data/cnvpanelizer/bioconda_cnvpanelizer.yaml +++ b/data/cnvpanelizer/bioconda_cnvpanelizer.yaml @@ -9,7 +9,6 @@ description: A method that allows for the use of a collection of non-matched nor home: https://bioconductor.org/packages/3.10/bioc/html/CNVPanelizer.html identifiers: - biotools:cnvpanelizer -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-cnvpanelizer diff --git a/data/cogps/bioconda_cogps.yaml b/data/cogps/bioconda_cogps.yaml index a99f5390cb544..6b7488bf3ce19 100644 --- a/data/cogps/bioconda_cogps.yaml +++ b/data/cogps/bioconda_cogps.yaml @@ -4,7 +4,6 @@ description: Gene Set Enrichment Analysis of P-value based statistics for outlie home: https://bioconductor.org/packages/3.10/bioc/html/coGPS.html identifiers: - biotools:cogps -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-cogps diff --git a/data/convert/bioconda_convert.yaml b/data/convert/bioconda_convert.yaml index 6ef424901d98e..44fa2e6447a59 100644 --- a/data/convert/bioconda_convert.yaml +++ b/data/convert/bioconda_convert.yaml @@ -3,7 +3,6 @@ description: Define coerce methods for microarray data objects. home: https://bioconductor.org/packages/3.10/bioc/html/convert.html identifiers: - biotools:convert -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-convert diff --git a/data/correp/bioconda_correp.yaml b/data/correp/bioconda_correp.yaml index 1fb71025fcc8e..4ebb8c6c06f51 100644 --- a/data/correp/bioconda_correp.yaml +++ b/data/correp/bioconda_correp.yaml @@ -4,7 +4,6 @@ description: Multivariate correlation estimation and statistical inference. See home: https://bioconductor.org/packages/3.10/bioc/html/CORREP.html identifiers: - biotools:correp -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-correp diff --git a/data/covrna/bioconda_covrna.yaml b/data/covrna/bioconda_covrna.yaml index fd9c53c3656e4..424b3b31f6273 100644 --- a/data/covrna/bioconda_covrna.yaml +++ b/data/covrna/bioconda_covrna.yaml @@ -4,7 +4,6 @@ description: This package provides the analysis methods fourthcorner and RLQ ana home: https://bioconductor.org/packages/3.10/bioc/html/covRNA.html identifiers: - biotools:covrna -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-covrna diff --git a/data/cpvsnp/bioconda_cpvsnp.yaml b/data/cpvsnp/bioconda_cpvsnp.yaml index 232aea355d375..c1cf5e3a93928 100644 --- a/data/cpvsnp/bioconda_cpvsnp.yaml +++ b/data/cpvsnp/bioconda_cpvsnp.yaml @@ -9,7 +9,6 @@ description: Gene set analysis methods exist to combine SNP-level association p- home: https://bioconductor.org/packages/3.10/bioc/html/cpvSNP.html identifiers: - biotools:cpvsnp -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-cpvsnp summary: Gene set analysis methods for SNP association p-values that lie in genes diff --git a/data/ctc/bioconda_ctc.yaml b/data/ctc/bioconda_ctc.yaml index 2e53389b033c0..0d386d76ed31d 100644 --- a/data/ctc/bioconda_ctc.yaml +++ b/data/ctc/bioconda_ctc.yaml @@ -4,7 +4,6 @@ description: Tools for export and import classification trees and clusters to ot home: https://bioconductor.org/packages/3.10/bioc/html/ctc.html identifiers: - biotools:ctc -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-ctc diff --git a/data/dcgsa/bioconda_dcgsa.yaml b/data/dcgsa/bioconda_dcgsa.yaml index b51586f3b66fa..21b8d19877a96 100644 --- a/data/dcgsa/bioconda_dcgsa.yaml +++ b/data/dcgsa/bioconda_dcgsa.yaml @@ -9,7 +9,6 @@ description: Distance-correlation based Gene Set Analysis for longitudinal gene home: https://bioconductor.org/packages/3.10/bioc/html/dcGSA.html identifiers: - biotools:dcgsa -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-dcgsa diff --git a/data/ddct/bioconda_ddct.yaml b/data/ddct/bioconda_ddct.yaml index 8194bc9b64a95..cfaa8ad3cc29a 100644 --- a/data/ddct/bioconda_ddct.yaml +++ b/data/ddct/bioconda_ddct.yaml @@ -11,7 +11,6 @@ description: The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to d home: https://bioconductor.org/packages/3.10/bioc/html/ddCt.html identifiers: - biotools:ddct -- doi:10.1038/nmeth.3252 license: LGPL-3 license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-ddct diff --git a/data/deformats/bioconda_deformats.yaml b/data/deformats/bioconda_deformats.yaml index 20a5175eb5faf..c9b2a34327272 100644 --- a/data/deformats/bioconda_deformats.yaml +++ b/data/deformats/bioconda_deformats.yaml @@ -4,7 +4,6 @@ description: Convert between different data formats used by differential gene ex home: https://bioconductor.org/packages/3.10/bioc/html/DEFormats.html identifiers: - biotools:deformats -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-deformats diff --git a/data/degreport/bioconda_degreport.yaml b/data/degreport/bioconda_degreport.yaml index d1834162d84e6..3826a7ed5a25e 100644 --- a/data/degreport/bioconda_degreport.yaml +++ b/data/degreport/bioconda_degreport.yaml @@ -6,7 +6,6 @@ description: Creation of a HTML report of differential expression analyses of co home: https://bioconductor.org/packages/3.10/bioc/html/DEGreport.html identifiers: - biotools:degreport -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-degreport diff --git a/data/demand/bioconda_demand.yaml b/data/demand/bioconda_demand.yaml index 585b2d185553c..f0756d5b444b9 100644 --- a/data/demand/bioconda_demand.yaml +++ b/data/demand/bioconda_demand.yaml @@ -6,7 +6,6 @@ description: DEMAND predicts Drug MoA by interrogating a cell context specific r home: https://bioconductor.org/packages/3.10/bioc/html/DeMAND.html identifiers: - biotools:demand -- doi:10.1038/nmeth.3252 license: file LICENSE license_file: LICENSE name: bioconductor-demand diff --git a/data/dfp/bioconda_dfp.yaml b/data/dfp/bioconda_dfp.yaml index 2eae76c44b4d9..15de95439f1d7 100644 --- a/data/dfp/bioconda_dfp.yaml +++ b/data/dfp/bioconda_dfp.yaml @@ -6,7 +6,6 @@ description: This package provides a supervised technique able to identify diffe home: https://bioconductor.org/packages/3.10/bioc/html/DFP.html identifiers: - biotools:dfp -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-dfp diff --git a/data/diffgeneanalysis/bioconda_diffgeneanalysis.yaml b/data/diffgeneanalysis/bioconda_diffgeneanalysis.yaml index ba773cec18bde..fa72e9c42d8a4 100644 --- a/data/diffgeneanalysis/bioconda_diffgeneanalysis.yaml +++ b/data/diffgeneanalysis/bioconda_diffgeneanalysis.yaml @@ -3,7 +3,6 @@ description: Analyze microarray data home: https://bioconductor.org/packages/3.10/bioc/html/diffGeneAnalysis.html identifiers: - biotools:diffgeneanalysis -- doi:10.1038/nmeth.3252 license: GPL license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-diffgeneanalysis diff --git a/data/director/bioconda_director.yaml b/data/director/bioconda_director.yaml index e6d12e15656b1..f76bdf4d2cfff 100644 --- a/data/director/bioconda_director.yaml +++ b/data/director/bioconda_director.yaml @@ -11,7 +11,6 @@ description: Director is an R package designed to streamline the visualization o home: https://bioconductor.org/packages/3.10/bioc/html/Director.html identifiers: - biotools:director -- doi:10.1038/nmeth.3252 license: GPL-3 + file LICENSE license_file: LICENSE name: bioconductor-director diff --git a/data/dnacopy/bioconda_dnacopy.yaml b/data/dnacopy/bioconda_dnacopy.yaml index 075842bf98920..d60b0a4ba795c 100644 --- a/data/dnacopy/bioconda_dnacopy.yaml +++ b/data/dnacopy/bioconda_dnacopy.yaml @@ -4,7 +4,6 @@ description: Implements the circular binary segmentation (CBS) algorithm to segm home: https://bioconductor.org/packages/3.10/bioc/html/DNAcopy.html identifiers: - biotools:dnacopy -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-dnacopy diff --git a/data/drugvsdisease/bioconda_drugvsdisease.yaml b/data/drugvsdisease/bioconda_drugvsdisease.yaml index b974d9a7d20be..3c28bbe1b2691 100644 --- a/data/drugvsdisease/bioconda_drugvsdisease.yaml +++ b/data/drugvsdisease/bioconda_drugvsdisease.yaml @@ -9,7 +9,6 @@ description: This package generates ranked lists of differential gene expression home: https://bioconductor.org/packages/3.10/bioc/html/DrugVsDisease.html identifiers: - biotools:drugvsdisease -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-drugvsdisease diff --git a/data/dyndoc/bioconda_dyndoc.yaml b/data/dyndoc/bioconda_dyndoc.yaml index ce48f29f4825e..d7879bc01857e 100644 --- a/data/dyndoc/bioconda_dyndoc.yaml +++ b/data/dyndoc/bioconda_dyndoc.yaml @@ -4,7 +4,6 @@ description: A set of functions to create and interact with dynamic documents an home: https://bioconductor.org/packages/3.10/bioc/html/DynDoc.html identifiers: - biotools:dyndoc -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-dyndoc summary: Dynamic document tools diff --git a/data/ebsea/bioconda_ebsea.yaml b/data/ebsea/bioconda_ebsea.yaml index 6ba4dcb2420fe..abce180096559 100644 --- a/data/ebsea/bioconda_ebsea.yaml +++ b/data/ebsea/bioconda_ebsea.yaml @@ -4,7 +4,6 @@ description: Calculates differential expression of genes based on exon counts of home: https://bioconductor.org/packages/3.10/bioc/html/EBSEA.html identifiers: - biotools:ebsea -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-ebsea diff --git a/data/encodexplorer/bioconda_encodexplorer.yaml b/data/encodexplorer/bioconda_encodexplorer.yaml index a5af9acf85e81..1b6b58d0356a9 100644 --- a/data/encodexplorer/bioconda_encodexplorer.yaml +++ b/data/encodexplorer/bioconda_encodexplorer.yaml @@ -5,7 +5,6 @@ description: This package allows user to quickly access ENCODE project files met home: https://bioconductor.org/packages/3.10/bioc/html/ENCODExplorer.html identifiers: - biotools:encodexplorer -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-encodexplorer summary: A compilation of ENCODE metadata diff --git a/data/ensembldb/bioconda_ensembldb.yaml b/data/ensembldb/bioconda_ensembldb.yaml index fd2c000b42d69..94a5722a2d83f 100644 --- a/data/ensembldb/bioconda_ensembldb.yaml +++ b/data/ensembldb/bioconda_ensembldb.yaml @@ -12,7 +12,6 @@ description: The package provides functions to create and use transcript centric home: https://bioconductor.org/packages/3.10/bioc/html/ensembldb.html identifiers: - biotools:ensembldb -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-ensembldb diff --git a/data/epivizrdata/bioconda_epivizrdata.yaml b/data/epivizrdata/bioconda_epivizrdata.yaml index 525770b0b0daf..673af036d0c32 100644 --- a/data/epivizrdata/bioconda_epivizrdata.yaml +++ b/data/epivizrdata/bioconda_epivizrdata.yaml @@ -3,7 +3,6 @@ description: Serve data from Bioconductor Objects through a WebSocket connection home: https://bioconductor.org/packages/3.10/bioc/html/epivizrData.html identifiers: - biotools:epivizrdata -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-epivizrdata diff --git a/data/epivizrserver/bioconda_epivizrserver.yaml b/data/epivizrserver/bioconda_epivizrserver.yaml index b07b194e2d81d..e2aeb7484a6f8 100644 --- a/data/epivizrserver/bioconda_epivizrserver.yaml +++ b/data/epivizrserver/bioconda_epivizrserver.yaml @@ -4,7 +4,6 @@ description: This package provides objects to manage WebSocket connections to ep home: https://bioconductor.org/packages/3.10/bioc/html/epivizrServer.html identifiers: - biotools:epivizrserver -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-epivizrserver diff --git a/data/epivizrstandalone/bioconda_epivizrstandalone.yaml b/data/epivizrstandalone/bioconda_epivizrstandalone.yaml index 36b3d7631ccff..3f7912d43bc28 100644 --- a/data/epivizrstandalone/bioconda_epivizrstandalone.yaml +++ b/data/epivizrstandalone/bioconda_epivizrstandalone.yaml @@ -6,7 +6,6 @@ description: This package imports the epiviz visualization JavaScript app for ge home: https://bioconductor.org/packages/3.10/bioc/html/epivizrStandalone.html identifiers: - biotools:epivizrstandalone -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-epivizrstandalone diff --git a/data/esetvis/bioconda_esetvis.yaml b/data/esetvis/bioconda_esetvis.yaml index 81262efcbb8f1..d8946c67d867d 100644 --- a/data/esetvis/bioconda_esetvis.yaml +++ b/data/esetvis/bioconda_esetvis.yaml @@ -6,7 +6,6 @@ description: Utility functions for visualization of expressionSet (or Summarized home: https://bioconductor.org/packages/3.10/bioc/html/esetVis.html identifiers: - biotools:esetvis -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-esetvis diff --git a/data/findmyfriends/bioconda_findmyfriends.yaml b/data/findmyfriends/bioconda_findmyfriends.yaml index b418f7be0de61..c9a987aba56ff 100644 --- a/data/findmyfriends/bioconda_findmyfriends.yaml +++ b/data/findmyfriends/bioconda_findmyfriends.yaml @@ -8,7 +8,6 @@ description: A framework for doing microbial comparative genomics in R. The main home: https://bioconductor.org/packages/3.10/bioc/html/FindMyFriends.html identifiers: - biotools:findmyfriends -- doi:10.1038/nmeth.3252 license: GPL (>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-findmyfriends diff --git a/data/fishalyser/bioconda_fishalyser.yaml b/data/fishalyser/bioconda_fishalyser.yaml index 3f5bd71e5e24c..1417e37993347 100644 --- a/data/fishalyser/bioconda_fishalyser.yaml +++ b/data/fishalyser/bioconda_fishalyser.yaml @@ -6,7 +6,6 @@ description: FISHalyseR provides functionality to process and analyse digital ce home: https://bioconductor.org/packages/3.10/bioc/html/FISHalyseR.html identifiers: - biotools:fishalyser -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-fishalyser summary: FISHalyseR a package for automated FISH quantification diff --git a/data/flagme/bioconda_flagme.yaml b/data/flagme/bioconda_flagme.yaml index b25328b0fa37d..9ab93ec661d86 100644 --- a/data/flagme/bioconda_flagme.yaml +++ b/data/flagme/bioconda_flagme.yaml @@ -4,7 +4,6 @@ description: Fragment-level analysis of gas chromatography - mass spectrometry m home: https://bioconductor.org/packages/3.10/bioc/html/flagme.html identifiers: - biotools:flagme -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-flagme diff --git a/data/flowbeads/bioconda_flowbeads.yaml b/data/flowbeads/bioconda_flowbeads.yaml index 233fb7b27fa8f..3c5b960b91a29 100644 --- a/data/flowbeads/bioconda_flowbeads.yaml +++ b/data/flowbeads/bioconda_flowbeads.yaml @@ -5,7 +5,6 @@ description: This package extends flowCore to provide functionality specific to home: https://bioconductor.org/packages/3.10/bioc/html/flowBeads.html identifiers: - biotools:flowbeads -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-flowbeads summary: 'flowBeads: Analysis of flow bead data' diff --git a/data/flowmatch/bioconda_flowmatch.yaml b/data/flowmatch/bioconda_flowmatch.yaml index 1a5cb6012377f..44e3714ae9f7f 100644 --- a/data/flowmatch/bioconda_flowmatch.yaml +++ b/data/flowmatch/bioconda_flowmatch.yaml @@ -4,7 +4,6 @@ description: Matching cell populations and building meta-clusters and templates home: https://bioconductor.org/packages/3.10/bioc/html/flowMatch.html identifiers: - biotools:flowmatch -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-flowmatch summary: Matching and meta-clustering in flow cytometry diff --git a/data/flowploidy/bioconda_flowploidy.yaml b/data/flowploidy/bioconda_flowploidy.yaml index c9a40c1c277db..3cddc5ac4ed29 100644 --- a/data/flowploidy/bioconda_flowploidy.yaml +++ b/data/flowploidy/bioconda_flowploidy.yaml @@ -5,7 +5,6 @@ description: Determine sample ploidy via flow cytometry histogram analysis. Read home: https://bioconductor.org/packages/3.10/bioc/html/flowPloidy.html identifiers: - biotools:flowploidy -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-flowploidy diff --git a/data/gcrisprtools/bioconda_gcrisprtools.yaml b/data/gcrisprtools/bioconda_gcrisprtools.yaml index b15018bfe51d2..88e9475e89df3 100644 --- a/data/gcrisprtools/bioconda_gcrisprtools.yaml +++ b/data/gcrisprtools/bioconda_gcrisprtools.yaml @@ -7,7 +7,6 @@ description: Set of tools for evaluating pooled high-throughput screening experi home: https://bioconductor.org/packages/3.10/bioc/html/gCrisprTools.html identifiers: - biotools:gcrisprtools -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-gcrisprtools summary: Suite of Functions for Pooled Crispr Screen QC and Analysis diff --git a/data/genbankr/bioconda_genbankr.yaml b/data/genbankr/bioconda_genbankr.yaml index 10242b77b4e6f..821d9ff871b1c 100644 --- a/data/genbankr/bioconda_genbankr.yaml +++ b/data/genbankr/bioconda_genbankr.yaml @@ -3,7 +3,6 @@ description: Reads Genbank files. home: https://bioconductor.org/packages/3.10/bioc/html/genbankr.html identifiers: - biotools:genbankr -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genbankr summary: Parsing GenBank files into semantically useful objects diff --git a/data/genefilter/bioconda_genefilter.yaml b/data/genefilter/bioconda_genefilter.yaml index b9fd7945a6e72..f344bc13d0f14 100644 --- a/data/genefilter/bioconda_genefilter.yaml +++ b/data/genefilter/bioconda_genefilter.yaml @@ -3,7 +3,6 @@ description: Some basic functions for filtering genes. home: https://bioconductor.org/packages/3.10/bioc/html/genefilter.html identifiers: - biotools:genefilter -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genefilter summary: 'genefilter: methods for filtering genes from high-throughput experiments' diff --git a/data/genemeta/bioconda_genemeta.yaml b/data/genemeta/bioconda_genemeta.yaml index ca5e52298701d..53c7964ebff1f 100644 --- a/data/genemeta/bioconda_genemeta.yaml +++ b/data/genemeta/bioconda_genemeta.yaml @@ -4,7 +4,6 @@ description: A collection of meta-analysis tools for analysing high throughput e home: https://bioconductor.org/packages/3.10/bioc/html/GeneMeta.html identifiers: - biotools:genemeta -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genemeta summary: MetaAnalysis for High Throughput Experiments diff --git a/data/geneplast/bioconda_geneplast.yaml b/data/geneplast/bioconda_geneplast.yaml index 656e7332fffe1..40f5353042d48 100644 --- a/data/geneplast/bioconda_geneplast.yaml +++ b/data/geneplast/bioconda_geneplast.yaml @@ -7,7 +7,6 @@ description: Geneplast is designed for evolutionary and plasticity analysis base home: https://bioconductor.org/packages/3.10/bioc/html/geneplast.html identifiers: - biotools:geneplast -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-geneplast diff --git a/data/geneplotter/bioconda_geneplotter.yaml b/data/geneplotter/bioconda_geneplotter.yaml index 469a66720e2b2..d8c3c3a2b16be 100644 --- a/data/geneplotter/bioconda_geneplotter.yaml +++ b/data/geneplotter/bioconda_geneplotter.yaml @@ -3,7 +3,6 @@ description: Functions for plotting genomic data home: https://bioconductor.org/packages/3.10/bioc/html/geneplotter.html identifiers: - biotools:geneplotter -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-geneplotter summary: Graphics related functions for Bioconductor diff --git a/data/geneticsdesign/bioconda_geneticsdesign.yaml b/data/geneticsdesign/bioconda_geneticsdesign.yaml index ce0b35c438422..a38938baf49f2 100644 --- a/data/geneticsdesign/bioconda_geneticsdesign.yaml +++ b/data/geneticsdesign/bioconda_geneticsdesign.yaml @@ -4,7 +4,6 @@ description: This package contains functions useful for designing genetics studi home: https://bioconductor.org/packages/3.10/bioc/html/GeneticsDesign.html identifiers: - biotools:geneticsdesign -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-geneticsdesign diff --git a/data/genomeinfodb/bioconda_genomeinfodb.yaml b/data/genomeinfodb/bioconda_genomeinfodb.yaml index 878730d3670ee..5c0ccc5d44e35 100644 --- a/data/genomeinfodb/bioconda_genomeinfodb.yaml +++ b/data/genomeinfodb/bioconda_genomeinfodb.yaml @@ -6,7 +6,6 @@ description: Contains data and functions that define and allow translation betwe home: https://bioconductor.org/packages/3.10/bioc/html/GenomeInfoDb.html identifiers: - biotools:genomeinfodb -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genomeinfodb summary: Utilities for manipulating chromosome names, including modifying them to diff --git a/data/genomeintervals/bioconda_genomeintervals.yaml b/data/genomeintervals/bioconda_genomeintervals.yaml index 3e358ab018467..286f9c959b08f 100644 --- a/data/genomeintervals/bioconda_genomeintervals.yaml +++ b/data/genomeintervals/bioconda_genomeintervals.yaml @@ -5,7 +5,6 @@ description: 'This package defines classes for representing genomic intervals an home: https://bioconductor.org/packages/3.10/bioc/html/genomeIntervals.html identifiers: - biotools:genomeintervals -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genomeintervals summary: Operations on genomic intervals diff --git a/data/genomicfiles/bioconda_genomicfiles.yaml b/data/genomicfiles/bioconda_genomicfiles.yaml index 22bb0a4821b94..17951a3917c44 100644 --- a/data/genomicfiles/bioconda_genomicfiles.yaml +++ b/data/genomicfiles/bioconda_genomicfiles.yaml @@ -5,7 +5,6 @@ description: This package provides infrastructure for parallel computations dist home: https://bioconductor.org/packages/3.10/bioc/html/GenomicFiles.html identifiers: - biotools:genomicfiles -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genomicfiles summary: Distributed computing by file or by range diff --git a/data/genominator/bioconda_genominator.yaml b/data/genominator/bioconda_genominator.yaml index ab0eb7f144513..d317d24dff085 100644 --- a/data/genominator/bioconda_genominator.yaml +++ b/data/genominator/bioconda_genominator.yaml @@ -3,7 +3,6 @@ description: Tools for storing, accessing, analyzing and visualizing genomic dat home: https://bioconductor.org/packages/3.10/bioc/html/Genominator.html identifiers: - biotools:genominator -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genominator summary: Analyze, manage and store genomic data diff --git a/data/genoset/bioconda_genoset.yaml b/data/genoset/bioconda_genoset.yaml index 84bb19ad576f8..a914f14eb66ea 100644 --- a/data/genoset/bioconda_genoset.yaml +++ b/data/genoset/bioconda_genoset.yaml @@ -7,7 +7,6 @@ description: GenoSet provides an extension of the RangedSummarizedExperiment cla home: https://bioconductor.org/packages/3.10/bioc/html/genoset.html identifiers: - biotools:genoset -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-genoset summary: A RangedSummarizedExperiment with methods for copy number analysis diff --git a/data/geosubmission/bioconda_geosubmission.yaml b/data/geosubmission/bioconda_geosubmission.yaml index ad30ac1824819..721d30c1dc102 100644 --- a/data/geosubmission/bioconda_geosubmission.yaml +++ b/data/geosubmission/bioconda_geosubmission.yaml @@ -4,7 +4,6 @@ description: Helps to easily submit a microarray dataset and the associated samp home: https://bioconductor.org/packages/3.10/bioc/html/GEOsubmission.html identifiers: - biotools:geosubmission -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-geosubmission diff --git a/data/ggbase/bioconda_ggbase.yaml b/data/ggbase/bioconda_ggbase.yaml index b9e79abc18b67..8e36e01774e0a 100644 --- a/data/ggbase/bioconda_ggbase.yaml +++ b/data/ggbase/bioconda_ggbase.yaml @@ -3,7 +3,6 @@ description: infrastructure home: https://bioconductor.org/packages/3.10/bioc/html/GGBase.html identifiers: - biotools:ggbase -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-ggbase summary: GGBase infrastructure for genetics of gene expression package GGtools diff --git a/data/ggcyto/bioconda_ggcyto.yaml b/data/ggcyto/bioconda_ggcyto.yaml index 524a20f8973a5..8e6171f2c46f3 100644 --- a/data/ggcyto/bioconda_ggcyto.yaml +++ b/data/ggcyto/bioconda_ggcyto.yaml @@ -6,7 +6,6 @@ description: With the dedicated fortify method implemented for flowSet, ncdfFlow home: https://bioconductor.org/packages/3.10/bioc/html/ggcyto.html identifiers: - biotools:ggcyto -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-ggcyto summary: Visualize Cytometry data with ggplot diff --git a/data/gmrp/bioconda_gmrp.yaml b/data/gmrp/bioconda_gmrp.yaml index b1b975daeecf0..489a4fccbbdeb 100644 --- a/data/gmrp/bioconda_gmrp.yaml +++ b/data/gmrp/bioconda_gmrp.yaml @@ -5,7 +5,6 @@ description: Perform Mendelian randomization analysis of multiple SNPs to determ home: https://bioconductor.org/packages/3.10/bioc/html/GMRP.html identifiers: - biotools:gmrp -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-gmrp diff --git a/data/gotools/bioconda_gotools.yaml b/data/gotools/bioconda_gotools.yaml index fa04086c0ee20..075df8e930885 100644 --- a/data/gotools/bioconda_gotools.yaml +++ b/data/gotools/bioconda_gotools.yaml @@ -4,7 +4,6 @@ description: Wraper functions for description/comparison of oligo ID list using home: https://bioconductor.org/packages/3.10/bioc/html/goTools.html identifiers: - biotools:gotools -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-gotools diff --git a/data/graph/bioconda_graph.yaml b/data/graph/bioconda_graph.yaml index 2a19b196aed57..888da34a9a1b6 100644 --- a/data/graph/bioconda_graph.yaml +++ b/data/graph/bioconda_graph.yaml @@ -3,7 +3,6 @@ description: A package that implements some simple graph handling capabilities. home: https://bioconductor.org/packages/3.10/bioc/html/graph.html identifiers: - biotools:graph -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-graph summary: 'graph: A package to handle graph data structures' diff --git a/data/grmetrics/bioconda_grmetrics.yaml b/data/grmetrics/bioconda_grmetrics.yaml index d21a7be3c63e7..c4f69b3973fad 100644 --- a/data/grmetrics/bioconda_grmetrics.yaml +++ b/data/grmetrics/bioconda_grmetrics.yaml @@ -4,7 +4,6 @@ description: Functions for calculating and visualizing growth-rate inhibition (G home: https://bioconductor.org/packages/3.10/bioc/html/GRmetrics.html identifiers: - biotools:grmetrics -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-grmetrics diff --git a/data/gseabase/bioconda_gseabase.yaml b/data/gseabase/bioconda_gseabase.yaml index 4a3a4a2044eeb..ac591c8217c37 100644 --- a/data/gseabase/bioconda_gseabase.yaml +++ b/data/gseabase/bioconda_gseabase.yaml @@ -4,7 +4,6 @@ description: This package provides classes and methods to support Gene Set Enric home: https://bioconductor.org/packages/3.10/bioc/html/GSEABase.html identifiers: - biotools:gseabase -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-gseabase summary: Gene set enrichment data structures and methods diff --git a/data/gsri/bioconda_gsri.yaml b/data/gsri/bioconda_gsri.yaml index ebdcb882105d8..3bad325df2977 100644 --- a/data/gsri/bioconda_gsri.yaml +++ b/data/gsri/bioconda_gsri.yaml @@ -4,7 +4,6 @@ description: The GSRI package estimates the number of differentially expressed g home: https://bioconductor.org/packages/3.10/bioc/html/GSRI.html identifiers: - biotools:gsri -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-gsri diff --git a/data/hdf5array/bioconda_hdf5array.yaml b/data/hdf5array/bioconda_hdf5array.yaml index f494ec763a1a3..934ef5e1c2608 100644 --- a/data/hdf5array/bioconda_hdf5array.yaml +++ b/data/hdf5array/bioconda_hdf5array.yaml @@ -9,7 +9,6 @@ description: Implements the HDF5Array and TENxMatrix classes, 2 convenient and m home: https://bioconductor.org/packages/3.10/bioc/html/HDF5Array.html identifiers: - biotools:hdf5array -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-hdf5array summary: HDF5 backend for DelayedArray objects diff --git a/data/heatplus/bioconda_heatplus.yaml b/data/heatplus/bioconda_heatplus.yaml index 56e6546e4a00c..3ab7c08739483 100644 --- a/data/heatplus/bioconda_heatplus.yaml +++ b/data/heatplus/bioconda_heatplus.yaml @@ -7,7 +7,6 @@ description: Display a rectangular heatmap (intensity plot) of a data matrix. By home: https://bioconductor.org/packages/3.10/bioc/html/Heatplus.html identifiers: - biotools:heatplus -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-heatplus diff --git a/data/helloranges/bioconda_helloranges.yaml b/data/helloranges/bioconda_helloranges.yaml index edd5522abe8e5..a01a63d248652 100644 --- a/data/helloranges/bioconda_helloranges.yaml +++ b/data/helloranges/bioconda_helloranges.yaml @@ -5,7 +5,6 @@ description: Translates bedtools command-line invocations to R code calling func home: https://bioconductor.org/packages/3.10/bioc/html/HelloRanges.html identifiers: - biotools:helloranges -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-helloranges diff --git a/data/help/bioconda_help.yaml b/data/help/bioconda_help.yaml index ba11a2bbc7e76..7bc3ecc9550a1 100644 --- a/data/help/bioconda_help.yaml +++ b/data/help/bioconda_help.yaml @@ -4,7 +4,6 @@ description: The package contains a modular pipeline for analysis of HELP microa home: https://bioconductor.org/packages/3.10/bioc/html/HELP.html identifiers: - biotools:help -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-help diff --git a/data/hiannotator/bioconda_hiannotator.yaml b/data/hiannotator/bioconda_hiannotator.yaml index a41ad5a70b954..127a0b766c749 100644 --- a/data/hiannotator/bioconda_hiannotator.yaml +++ b/data/hiannotator/bioconda_hiannotator.yaml @@ -12,7 +12,6 @@ description: 'hiAnnotator contains set of functions which allow users to annotat home: https://bioconductor.org/packages/3.10/bioc/html/hiAnnotator.html identifiers: - biotools:hiannotator -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hiannotator diff --git a/data/hmmcopy/bioconda_hmmcopy.yaml b/data/hmmcopy/bioconda_hmmcopy.yaml index 7ecbc62913150..238f6d709b04f 100644 --- a/data/hmmcopy/bioconda_hmmcopy.yaml +++ b/data/hmmcopy/bioconda_hmmcopy.yaml @@ -6,7 +6,6 @@ description: Corrects GC and mappability biases for readcounts (i.e. coverage) i home: https://bioconductor.org/packages/3.10/bioc/html/HMMcopy.html identifiers: - biotools:hmmcopy -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hmmcopy diff --git a/data/hopach/bioconda_hopach.yaml b/data/hopach/bioconda_hopach.yaml index eb70ce664cd53..e2f580bdd9e70 100644 --- a/data/hopach/bioconda_hopach.yaml +++ b/data/hopach/bioconda_hopach.yaml @@ -9,7 +9,6 @@ description: The HOPACH clustering algorithm builds a hierarchical tree of clust home: https://bioconductor.org/packages/3.10/bioc/html/hopach.html identifiers: - biotools:hopach -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hopach diff --git a/data/hpar/bioconda_hpar.yaml b/data/hpar/bioconda_hpar.yaml index e7d591756fba9..fe6aaebe15ee9 100644 --- a/data/hpar/bioconda_hpar.yaml +++ b/data/hpar/bioconda_hpar.yaml @@ -4,7 +4,6 @@ description: The hpar package provides a simple R interface to and data from the home: https://bioconductor.org/packages/3.10/bioc/html/hpar.html identifiers: - biotools:hpar -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-hpar summary: Human Protein Atlas in R diff --git a/data/hybridmtest/bioconda_hybridmtest.yaml b/data/hybridmtest/bioconda_hybridmtest.yaml index 0c851c92e07b3..72d6385938ed4 100644 --- a/data/hybridmtest/bioconda_hybridmtest.yaml +++ b/data/hybridmtest/bioconda_hybridmtest.yaml @@ -10,7 +10,6 @@ description: Performs hybrid multiple testing that incorporates method selection home: https://bioconductor.org/packages/3.10/bioc/html/HybridMTest.html identifiers: - biotools:hybridmtest -- doi:10.1038/nmeth.3252 license: GPL Version 2 or later license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hybridmtest diff --git a/data/hyperdraw/bioconda_hyperdraw.yaml b/data/hyperdraw/bioconda_hyperdraw.yaml index 889c54b76c336..7e6890de9356e 100644 --- a/data/hyperdraw/bioconda_hyperdraw.yaml +++ b/data/hyperdraw/bioconda_hyperdraw.yaml @@ -3,7 +3,6 @@ description: Functions for visualizing hypergraphs. home: https://bioconductor.org/packages/3.10/bioc/html/hyperdraw.html identifiers: - biotools:hyperdraw -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-hyperdraw diff --git a/data/hypergraph/bioconda_hypergraph.yaml b/data/hypergraph/bioconda_hypergraph.yaml index c7391147bc4bf..b384e73094f09 100644 --- a/data/hypergraph/bioconda_hypergraph.yaml +++ b/data/hypergraph/bioconda_hypergraph.yaml @@ -4,7 +4,6 @@ description: A package that implements some simple capabilities for representing home: https://bioconductor.org/packages/3.10/bioc/html/hypergraph.html identifiers: - biotools:hypergraph -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-hypergraph summary: A package providing hypergraph data structures diff --git a/data/ibh/bioconda_ibh.yaml b/data/ibh/bioconda_ibh.yaml index 449cfdca17ce2..b4b4ecc8e2c16 100644 --- a/data/ibh/bioconda_ibh.yaml +++ b/data/ibh/bioconda_ibh.yaml @@ -6,7 +6,6 @@ description: This package contains methods for calculating Interaction Based Hom home: https://bioconductor.org/packages/3.10/bioc/html/ibh.html identifiers: - biotools:ibh -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-ibh diff --git a/data/icens/bioconda_icens.yaml b/data/icens/bioconda_icens.yaml index 65e6d79dc446e..1df61685a9eea 100644 --- a/data/icens/bioconda_icens.yaml +++ b/data/icens/bioconda_icens.yaml @@ -3,7 +3,6 @@ description: Many functions for computing the NPMLE for censored and truncated d home: https://bioconductor.org/packages/3.10/bioc/html/Icens.html identifiers: - biotools:icens -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-icens summary: NPMLE for Censored and Truncated Data diff --git a/data/ideoviz/bioconda_ideoviz.yaml b/data/ideoviz/bioconda_ideoviz.yaml index 5aad3108f3439..0694ba63a1d22 100644 --- a/data/ideoviz/bioconda_ideoviz.yaml +++ b/data/ideoviz/bioconda_ideoviz.yaml @@ -4,7 +4,6 @@ description: Plots data associated with arbitrary genomic intervals along chromo home: https://bioconductor.org/packages/3.10/bioc/html/IdeoViz.html identifiers: - biotools:ideoviz -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-ideoviz diff --git a/data/idiogram/bioconda_idiogram.yaml b/data/idiogram/bioconda_idiogram.yaml index 8f53602b0f437..b9cb451c91f9a 100644 --- a/data/idiogram/bioconda_idiogram.yaml +++ b/data/idiogram/bioconda_idiogram.yaml @@ -3,7 +3,6 @@ description: A package for plotting genomic data by chromosomal location home: https://bioconductor.org/packages/3.10/bioc/html/idiogram.html identifiers: - biotools:idiogram -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-idiogram diff --git a/data/imagehts/bioconda_imagehts.yaml b/data/imagehts/bioconda_imagehts.yaml index 11cb687c69dc1..33a14f0906a35 100644 --- a/data/imagehts/bioconda_imagehts.yaml +++ b/data/imagehts/bioconda_imagehts.yaml @@ -8,7 +8,6 @@ description: imageHTS is an R package dedicated to the analysis of high-throughp home: https://bioconductor.org/packages/3.10/bioc/html/imageHTS.html identifiers: - biotools:imagehts -- doi:10.1038/nmeth.3252 license: LGPL-2.1 license_file: /lib/R/share/licenses/LGPL-2.1 name: bioconductor-imagehts diff --git a/data/inpower/bioconda_inpower.yaml b/data/inpower/bioconda_inpower.yaml index 6cf3575b673ff..ded11eaf49273 100644 --- a/data/inpower/bioconda_inpower.yaml +++ b/data/inpower/bioconda_inpower.yaml @@ -4,7 +4,6 @@ description: An R package for computing the number of susceptibility SNPs and po home: https://bioconductor.org/packages/3.10/bioc/html/INPower.html identifiers: - biotools:inpower -- doi:10.1038/nmeth.3252 license: GPL-2 + file LICENSE license_file: LICENSE name: bioconductor-inpower diff --git a/data/interactivedisplay/bioconda_interactivedisplay.yaml b/data/interactivedisplay/bioconda_interactivedisplay.yaml index 5e36697abc908..240ac885bb9ac 100644 --- a/data/interactivedisplay/bioconda_interactivedisplay.yaml +++ b/data/interactivedisplay/bioconda_interactivedisplay.yaml @@ -4,7 +4,6 @@ description: The interactiveDisplay package contains the methods needed to gener home: https://bioconductor.org/packages/3.10/bioc/html/interactiveDisplay.html identifiers: - biotools:interactivedisplay -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-interactivedisplay summary: Package for enabling powerful shiny web displays of Bioconductor objects diff --git a/data/interactivedisplaybase/bioconda_interactivedisplaybase.yaml b/data/interactivedisplaybase/bioconda_interactivedisplaybase.yaml index 248b3285b9a0d..89083fd4cbe07 100644 --- a/data/interactivedisplaybase/bioconda_interactivedisplaybase.yaml +++ b/data/interactivedisplaybase/bioconda_interactivedisplaybase.yaml @@ -4,7 +4,6 @@ description: The interactiveDisplayBase package contains the the basic methods n home: https://bioconductor.org/packages/3.10/bioc/html/interactiveDisplayBase.html identifiers: - biotools:interactivedisplaybase -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-interactivedisplaybase summary: Base package for enabling powerful shiny web displays of Bioconductor objects diff --git a/data/ioniser/bioconda_ioniser.yaml b/data/ioniser/bioconda_ioniser.yaml index be6d8a5010cef..df8f661767911 100644 --- a/data/ioniser/bioconda_ioniser.yaml +++ b/data/ioniser/bioconda_ioniser.yaml @@ -7,7 +7,6 @@ description: IONiseR provides tools for the quality assessment of Oxford Nanopor home: https://bioconductor.org/packages/3.10/bioc/html/IONiseR.html identifiers: - biotools:ioniser -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-ioniser diff --git a/data/isolde/bioconda_isolde.yaml b/data/isolde/bioconda_isolde.yaml index 57afb7e9d37f9..1beeaac689ecc 100644 --- a/data/isolde/bioconda_isolde.yaml +++ b/data/isolde/bioconda_isolde.yaml @@ -6,7 +6,6 @@ description: This package provides ISoLDE a new method for identifying imprinted home: https://bioconductor.org/packages/3.10/bioc/html/ISoLDE.html identifiers: - biotools:isolde -- doi:10.1038/nmeth.3252 license: GPL (>= 2.0) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-isolde diff --git a/data/keggorthology/bioconda_keggorthology.yaml b/data/keggorthology/bioconda_keggorthology.yaml index 7d5b1319689b2..9ee4c621bff00 100644 --- a/data/keggorthology/bioconda_keggorthology.yaml +++ b/data/keggorthology/bioconda_keggorthology.yaml @@ -4,7 +4,6 @@ description: graphical representation of the Feb 2010 KEGG Orthology. The KEGG o home: https://bioconductor.org/packages/3.10/bioc/html/keggorthology.html identifiers: - biotools:keggorthology -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-keggorthology summary: graph support for KO, KEGG Orthology diff --git a/data/kimod/bioconda_kimod.yaml b/data/kimod/bioconda_kimod.yaml index 449e1e1006dc0..7f8840611e365 100644 --- a/data/kimod/bioconda_kimod.yaml +++ b/data/kimod/bioconda_kimod.yaml @@ -16,7 +16,6 @@ description: 'This package allows to work with mixed omics data (transcriptomics home: https://bioconductor.org/packages/3.10/bioc/html/kimod.html identifiers: - biotools:kimod -- doi:10.1038/nmeth.3252 license: GPL (>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-kimod diff --git a/data/linc/bioconda_linc.yaml b/data/linc/bioconda_linc.yaml index 0becd678c150e..0d4950249f2f6 100644 --- a/data/linc/bioconda_linc.yaml +++ b/data/linc/bioconda_linc.yaml @@ -6,7 +6,6 @@ description: This package provides methods to compute co-expression networks of home: https://bioconductor.org/packages/3.10/bioc/html/LINC.html identifiers: - biotools:linc -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-linc summary: co-expression of lincRNAs and protein-coding genes diff --git a/data/liquidassociation/bioconda_liquidassociation.yaml b/data/liquidassociation/bioconda_liquidassociation.yaml index 280a5f664bdf6..9e480a9a72694 100644 --- a/data/liquidassociation/bioconda_liquidassociation.yaml +++ b/data/liquidassociation/bioconda_liquidassociation.yaml @@ -5,7 +5,6 @@ description: The package contains functions for calculate direct and model-based home: https://bioconductor.org/packages/3.10/bioc/html/LiquidAssociation.html identifiers: - biotools:liquidassociation -- doi:10.1038/nmeth.3252 license: GPL (>=3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-liquidassociation diff --git a/data/lmgene/bioconda_lmgene.yaml b/data/lmgene/bioconda_lmgene.yaml index d2abbca742baa..576dd416af95e 100644 --- a/data/lmgene/bioconda_lmgene.yaml +++ b/data/lmgene/bioconda_lmgene.yaml @@ -4,7 +4,6 @@ description: LMGene package for analysis of microarray data using a linear model home: https://bioconductor.org/packages/3.10/bioc/html/LMGene.html identifiers: - biotools:lmgene -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-lmgene diff --git a/data/logitt/bioconda_logitt.yaml b/data/logitt/bioconda_logitt.yaml index bdfcfaeb02bf8..16cabda9961a4 100644 --- a/data/logitt/bioconda_logitt.yaml +++ b/data/logitt/bioconda_logitt.yaml @@ -6,7 +6,6 @@ description: The logitT library implements the Logit-t algorithm introduced in - home: https://bioconductor.org/packages/3.10/bioc/html/logitT.html identifiers: - biotools:logitt -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-logitt diff --git a/data/lol/bioconda_lol.yaml b/data/lol/bioconda_lol.yaml index db4e27c1dd833..76b67fa341239 100644 --- a/data/lol/bioconda_lol.yaml +++ b/data/lol/bioconda_lol.yaml @@ -3,7 +3,6 @@ description: Various optimization methods for Lasso inference with matrix warppe home: https://bioconductor.org/packages/3.10/bioc/html/lol.html identifiers: - biotools:lol -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-lol diff --git a/data/lpeadj/bioconda_lpeadj.yaml b/data/lpeadj/bioconda_lpeadj.yaml index 0bc576e6bfccc..17bdb90313876 100644 --- a/data/lpeadj/bioconda_lpeadj.yaml +++ b/data/lpeadj/bioconda_lpeadj.yaml @@ -7,7 +7,6 @@ description: Two options are added to the LPE algorithm. The original LPE method home: https://bioconductor.org/packages/3.10/bioc/html/LPEadj.html identifiers: - biotools:lpeadj -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-lpeadj diff --git a/data/macorrplot/bioconda_macorrplot.yaml b/data/macorrplot/bioconda_macorrplot.yaml index d116bcba3beae..306efa867df33 100644 --- a/data/macorrplot/bioconda_macorrplot.yaml +++ b/data/macorrplot/bioconda_macorrplot.yaml @@ -4,7 +4,6 @@ description: Graphically displays correlation in microarray data that is due to home: https://bioconductor.org/packages/3.10/bioc/html/maCorrPlot.html identifiers: - biotools:macorrplot -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-macorrplot diff --git a/data/maigespack/bioconda_maigespack.yaml b/data/maigespack/bioconda_maigespack.yaml index 96c32f0970a4e..b040c359e7da3 100644 --- a/data/maigespack/bioconda_maigespack.yaml +++ b/data/maigespack/bioconda_maigespack.yaml @@ -4,7 +4,6 @@ description: This package uses functions of various other packages together with home: https://bioconductor.org/packages/3.10/bioc/html/maigesPack.html identifiers: - biotools:maigespack -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-maigespack diff --git a/data/manta/bioconda_manta.yaml b/data/manta/bioconda_manta.yaml index 2ac49b1740e9c..13b181599a46f 100644 --- a/data/manta/bioconda_manta.yaml +++ b/data/manta/bioconda_manta.yaml @@ -3,7 +3,6 @@ description: Tools for robust comparative metatranscriptomics. home: https://bioconductor.org/packages/3.10/bioc/html/manta.html identifiers: - biotools:manta -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-manta summary: Microbial Assemblage Normalized Transcript Analysis diff --git a/data/mantelcorr/bioconda_mantelcorr.yaml b/data/mantelcorr/bioconda_mantelcorr.yaml index a630a6c5c979c..b49b1f859340c 100644 --- a/data/mantelcorr/bioconda_mantelcorr.yaml +++ b/data/mantelcorr/bioconda_mantelcorr.yaml @@ -4,7 +4,6 @@ description: Computes Mantel cluster correlations from a (p x n) numeric data ma home: https://bioconductor.org/packages/3.10/bioc/html/MantelCorr.html identifiers: - biotools:mantelcorr -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-mantelcorr diff --git a/data/matter/bioconda_matter.yaml b/data/matter/bioconda_matter.yaml index 5b142efd5a2d1..da50c9e55c4d4 100644 --- a/data/matter/bioconda_matter.yaml +++ b/data/matter/bioconda_matter.yaml @@ -4,7 +4,6 @@ description: Memory-efficient reading, writing, and manipulation of structured b home: https://bioconductor.org/packages/3.10/bioc/html/matter.html identifiers: - biotools:matter -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-matter summary: A framework for rapid prototyping with file-based data structures diff --git a/data/mcrestimate/bioconda_mcrestimate.yaml b/data/mcrestimate/bioconda_mcrestimate.yaml index f1101c62cb090..b4d298b1cb494 100644 --- a/data/mcrestimate/bioconda_mcrestimate.yaml +++ b/data/mcrestimate/bioconda_mcrestimate.yaml @@ -4,7 +4,6 @@ description: This package includes a function for combining preprocessing and cl home: https://bioconductor.org/packages/3.10/bioc/html/MCRestimate.html identifiers: - biotools:mcrestimate -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-mcrestimate diff --git a/data/measurementerror.cor/bioconda_measurementerror.cor.yaml b/data/measurementerror.cor/bioconda_measurementerror.cor.yaml index 4c3ed6b14efa1..1f5945806570f 100644 --- a/data/measurementerror.cor/bioconda_measurementerror.cor.yaml +++ b/data/measurementerror.cor/bioconda_measurementerror.cor.yaml @@ -4,7 +4,6 @@ description: Two-stage measurement error model for correlation estimation with s home: https://bioconductor.org/packages/3.10/bioc/html/MeasurementError.cor.html identifiers: - biotools:measurementerror.cor -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-measurementerror.cor diff --git a/data/meshes/bioconda_meshes.yaml b/data/meshes/bioconda_meshes.yaml index 87e03c5d0cd1a..699615c081555 100644 --- a/data/meshes/bioconda_meshes.yaml +++ b/data/meshes/bioconda_meshes.yaml @@ -10,7 +10,6 @@ description: MeSH (Medical Subject Headings) is the NLM controlled vocabulary us home: https://bioconductor.org/packages/3.10/bioc/html/meshes.html identifiers: - biotools:meshes -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-meshes summary: MeSH Enrichment and Semantic analyses diff --git a/data/metaseq/bioconda_metaseq.yaml b/data/metaseq/bioconda_metaseq.yaml index 043dab458f4f5..409336456c6d2 100644 --- a/data/metaseq/bioconda_metaseq.yaml +++ b/data/metaseq/bioconda_metaseq.yaml @@ -4,7 +4,6 @@ description: The probabilities by one-sided NOISeq are combined by Fisher's meth home: https://bioconductor.org/packages/3.10/bioc/html/metaSeq.html identifiers: - biotools:metaseq -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-metaseq summary: Meta-analysis of RNA-Seq count data in multiple studies diff --git a/data/methtargetedngs/bioconda_methtargetedngs.yaml b/data/methtargetedngs/bioconda_methtargetedngs.yaml index 918b9330c29d5..4a68f2b696ec3 100644 --- a/data/methtargetedngs/bioconda_methtargetedngs.yaml +++ b/data/methtargetedngs/bioconda_methtargetedngs.yaml @@ -4,7 +4,6 @@ description: Perform step by step methylation analysis of Next Generation Sequen home: https://bioconductor.org/packages/3.10/bioc/html/MethTargetedNGS.html identifiers: - biotools:methtargetedngs -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-methtargetedngs summary: Perform Methylation Analysis on Next Generation Sequencing Data diff --git a/data/methyanalysis/bioconda_methyanalysis.yaml b/data/methyanalysis/bioconda_methyanalysis.yaml index 49aa13b12662a..296975876ffb2 100644 --- a/data/methyanalysis/bioconda_methyanalysis.yaml +++ b/data/methyanalysis/bioconda_methyanalysis.yaml @@ -6,7 +6,6 @@ description: The methyAnalysis package aims for the DNA methylation data analysi home: https://bioconductor.org/packages/3.10/bioc/html/methyAnalysis.html identifiers: - biotools:methyanalysis -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-methyanalysis summary: DNA methylation data analysis and visualization diff --git a/data/michip/bioconda_michip.yaml b/data/michip/bioconda_michip.yaml index a510adcb174bd..fe9d200edbdbc 100644 --- a/data/michip/bioconda_michip.yaml +++ b/data/michip/bioconda_michip.yaml @@ -6,7 +6,6 @@ description: This package takes the MiChip miRNA microarray .grp scanner output home: https://bioconductor.org/packages/3.10/bioc/html/MiChip.html identifiers: - biotools:michip -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-michip diff --git a/data/microrna/bioconda_microrna.yaml b/data/microrna/bioconda_microrna.yaml index 6c11b41592106..4f817ee2db7df 100644 --- a/data/microrna/bioconda_microrna.yaml +++ b/data/microrna/bioconda_microrna.yaml @@ -4,7 +4,6 @@ description: Different data resources for microRNAs and some functions for manip home: https://bioconductor.org/packages/3.10/bioc/html/microRNA.html identifiers: - biotools:microrna -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-microrna summary: Data and functions for dealing with microRNAs diff --git a/data/mirnatap/bioconda_mirnatap.yaml b/data/mirnatap/bioconda_mirnatap.yaml index 3f1d8860bf233..377b437ab7505 100644 --- a/data/mirnatap/bioconda_mirnatap.yaml +++ b/data/mirnatap/bioconda_mirnatap.yaml @@ -7,7 +7,6 @@ description: The package facilitates implementation of workflows requiring miRNA home: https://bioconductor.org/packages/3.10/bioc/html/miRNAtap.html identifiers: - biotools:mirnatap -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-mirnatap diff --git a/data/mlinterfaces/bioconda_mlinterfaces.yaml b/data/mlinterfaces/bioconda_mlinterfaces.yaml index b342af9f591fd..c66e772062a23 100644 --- a/data/mlinterfaces/bioconda_mlinterfaces.yaml +++ b/data/mlinterfaces/bioconda_mlinterfaces.yaml @@ -4,7 +4,6 @@ description: This package provides uniform interfaces to machine learning code f home: https://bioconductor.org/packages/3.10/bioc/html/MLInterfaces.html identifiers: - biotools:mlinterfaces -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-mlinterfaces diff --git a/data/mlseq/bioconda_mlseq.yaml b/data/mlseq/bioconda_mlseq.yaml index 6578955c57454..1aa98b74b3574 100644 --- a/data/mlseq/bioconda_mlseq.yaml +++ b/data/mlseq/bioconda_mlseq.yaml @@ -4,7 +4,6 @@ description: This package applies several machine learning methods, including SV home: https://bioconductor.org/packages/3.10/bioc/html/MLSeq.html identifiers: - biotools:mlseq -- doi:10.1038/nmeth.3252 license: GPL(>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-mlseq diff --git a/data/mmdiff2/bioconda_mmdiff2.yaml b/data/mmdiff2/bioconda_mmdiff2.yaml index 98cdb17d07c74..cb7720d2b69d1 100644 --- a/data/mmdiff2/bioconda_mmdiff2.yaml +++ b/data/mmdiff2/bioconda_mmdiff2.yaml @@ -5,7 +5,6 @@ description: This package detects statistically significant differences between home: https://bioconductor.org/packages/3.10/bioc/html/MMDiff2.html identifiers: - biotools:mmdiff2 -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-mmdiff2 summary: Statistical Testing for ChIP-Seq data sets diff --git a/data/motifdb/bioconda_motifdb.yaml b/data/motifdb/bioconda_motifdb.yaml index a85c91052bdca..cb43cfb01c2b7 100644 --- a/data/motifdb/bioconda_motifdb.yaml +++ b/data/motifdb/bioconda_motifdb.yaml @@ -4,7 +4,6 @@ description: More than 9900 annotated position frequency matrices from 14 public home: https://bioconductor.org/packages/3.10/bioc/html/MotifDb.html identifiers: - biotools:motifdb -- doi:10.1038/nmeth.3252 license: Artistic-2.0 | file LICENSE license_file: LICENSE name: bioconductor-motifdb diff --git a/data/motifstack/bioconda_motifstack.yaml b/data/motifstack/bioconda_motifstack.yaml index 0c71a5f9dd136..bc5a15e666ac0 100644 --- a/data/motifstack/bioconda_motifstack.yaml +++ b/data/motifstack/bioconda_motifstack.yaml @@ -6,7 +6,6 @@ description: The motifStack package is designed for graphic representation of mu home: https://bioconductor.org/packages/3.10/bioc/html/motifStack.html identifiers: - biotools:motifstack -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-motifstack diff --git a/data/motiv/bioconda_motiv.yaml b/data/motiv/bioconda_motiv.yaml index f6ae5daa0276a..35705f8a6172b 100644 --- a/data/motiv/bioconda_motiv.yaml +++ b/data/motiv/bioconda_motiv.yaml @@ -5,7 +5,6 @@ description: This package makes use of STAMP for comparing a set of motifs to a home: https://bioconductor.org/packages/3.10/bioc/html/MotIV.html identifiers: - biotools:motiv -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-motiv diff --git a/data/msmseda/bioconda_msmseda.yaml b/data/msmseda/bioconda_msmseda.yaml index bb46a577003cb..51a54376cba66 100644 --- a/data/msmseda/bioconda_msmseda.yaml +++ b/data/msmseda/bioconda_msmseda.yaml @@ -4,7 +4,6 @@ description: Exploratory data analysis to assess the quality of a set of LC-MS/M home: https://bioconductor.org/packages/3.10/bioc/html/msmsEDA.html identifiers: - biotools:msmseda -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-msmseda diff --git a/data/msnid/bioconda_msnid.yaml b/data/msnid/bioconda_msnid.yaml index b78336db6aacf..e4716620ee665 100644 --- a/data/msnid/bioconda_msnid.yaml +++ b/data/msnid/bioconda_msnid.yaml @@ -8,7 +8,6 @@ description: Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or home: https://bioconductor.org/packages/3.10/bioc/html/MSnID.html identifiers: - biotools:msnid -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-msnid summary: Utilities for Exploration and Assessment of Confidence of LC-MSn Proteomics diff --git a/data/multiscan/bioconda_multiscan.yaml b/data/multiscan/bioconda_multiscan.yaml index ff346b658eb9f..f48f5f767e87f 100644 --- a/data/multiscan/bioconda_multiscan.yaml +++ b/data/multiscan/bioconda_multiscan.yaml @@ -3,7 +3,6 @@ description: Estimates gene expressions from several laser scans of the same mic home: https://bioconductor.org/packages/3.10/bioc/html/multiscan.html identifiers: - biotools:multiscan -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-multiscan diff --git a/data/mvcclass/bioconda_mvcclass.yaml b/data/mvcclass/bioconda_mvcclass.yaml index 0077632fb1fcb..be71dbde69d92 100644 --- a/data/mvcclass/bioconda_mvcclass.yaml +++ b/data/mvcclass/bioconda_mvcclass.yaml @@ -3,7 +3,6 @@ description: Creates classes used in model-view-controller (MVC) design home: https://bioconductor.org/packages/3.10/bioc/html/MVCClass.html identifiers: - biotools:mvcclass -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-mvcclass diff --git a/data/mzid/bioconda_mzid.yaml b/data/mzid/bioconda_mzid.yaml index ceafd7ec57f85..230e9e3f75638 100644 --- a/data/mzid/bioconda_mzid.yaml +++ b/data/mzid/bioconda_mzid.yaml @@ -7,7 +7,6 @@ description: A parser for mzIdentML files implemented using the XML package. The home: https://bioconductor.org/packages/3.10/bioc/html/mzID.html identifiers: - biotools:mzid -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-mzid diff --git a/data/ncigraph/bioconda_ncigraph.yaml b/data/ncigraph/bioconda_ncigraph.yaml index 54bcb8fa35535..79cd7a7985b2b 100644 --- a/data/ncigraph/bioconda_ncigraph.yaml +++ b/data/ncigraph/bioconda_ncigraph.yaml @@ -4,7 +4,6 @@ description: Provides various methods to load the pathways from the NCI Pathways home: https://bioconductor.org/packages/3.10/bioc/html/NCIgraph.html identifiers: - biotools:ncigraph -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-ncigraph diff --git a/data/oligoclasses/bioconda_oligoclasses.yaml b/data/oligoclasses/bioconda_oligoclasses.yaml index a797f95fb83d3..d56a35ccb5987 100644 --- a/data/oligoclasses/bioconda_oligoclasses.yaml +++ b/data/oligoclasses/bioconda_oligoclasses.yaml @@ -4,7 +4,6 @@ description: This package contains class definitions, validity checks, and initi home: https://bioconductor.org/packages/3.10/bioc/html/oligoClasses.html identifiers: - biotools:oligoclasses -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-oligoclasses diff --git a/data/organismdbi/bioconda_organismdbi.yaml b/data/organismdbi/bioconda_organismdbi.yaml index 8e14f90c8534e..0e10ac3a90f4e 100644 --- a/data/organismdbi/bioconda_organismdbi.yaml +++ b/data/organismdbi/bioconda_organismdbi.yaml @@ -5,7 +5,6 @@ description: The package enables a simple unified interface to several annotatio home: https://bioconductor.org/packages/3.10/bioc/html/OrganismDbi.html identifiers: - biotools:organismdbi -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-organismdbi summary: Software to enable the smooth interfacing of different database packages diff --git a/data/paircompviz/bioconda_paircompviz.yaml b/data/paircompviz/bioconda_paircompviz.yaml index f7f1532878c51..c27d1cb9d352d 100644 --- a/data/paircompviz/bioconda_paircompviz.yaml +++ b/data/paircompviz/bioconda_paircompviz.yaml @@ -8,7 +8,6 @@ description: This package provides visualization of the results from the multipl home: https://bioconductor.org/packages/3.10/bioc/html/paircompviz.html identifiers: - biotools:paircompviz -- doi:10.1038/nmeth.3252 license: GPL (>=3.0) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-paircompviz diff --git a/data/parody/bioconda_parody.yaml b/data/parody/bioconda_parody.yaml index c892df3814730..14f9415375736 100644 --- a/data/parody/bioconda_parody.yaml +++ b/data/parody/bioconda_parody.yaml @@ -4,7 +4,6 @@ description: routines for univariate and multivariate outlier detection with a f home: https://bioconductor.org/packages/3.10/bioc/html/parody.html identifiers: - biotools:parody -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-parody summary: Parametric And Resistant Outlier DYtection diff --git a/data/pathostat/bioconda_pathostat.yaml b/data/pathostat/bioconda_pathostat.yaml index 948c736128a78..82592d0011cab 100644 --- a/data/pathostat/bioconda_pathostat.yaml +++ b/data/pathostat/bioconda_pathostat.yaml @@ -7,7 +7,6 @@ description: The purpose of this package is to perform Statistical Microbiome An home: https://bioconductor.org/packages/3.10/bioc/html/PathoStat.html identifiers: - biotools:pathostat -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-pathostat diff --git a/data/pathrender/bioconda_pathrender.yaml b/data/pathrender/bioconda_pathrender.yaml index 409d495392978..4d9b1d5a8cfc2 100644 --- a/data/pathrender/bioconda_pathrender.yaml +++ b/data/pathrender/bioconda_pathrender.yaml @@ -3,7 +3,6 @@ description: build graphs from pathway databases, render them by Rgraphviz. home: https://bioconductor.org/packages/3.10/bioc/html/pathRender.html identifiers: - biotools:pathrender -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-pathrender diff --git a/data/pcot2/bioconda_pcot2.yaml b/data/pcot2/bioconda_pcot2.yaml index 8db4e0ee44c74..03b0e4bc78208 100644 --- a/data/pcot2/bioconda_pcot2.yaml +++ b/data/pcot2/bioconda_pcot2.yaml @@ -6,7 +6,6 @@ description: PCOT2 is a permutation-based method for investigating changes in th home: https://bioconductor.org/packages/3.10/bioc/html/pcot2.html identifiers: - biotools:pcot2 -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-pcot2 diff --git a/data/pcpheno/bioconda_pcpheno.yaml b/data/pcpheno/bioconda_pcpheno.yaml index 40d1ff37f9924..b0900f887616e 100644 --- a/data/pcpheno/bioconda_pcpheno.yaml +++ b/data/pcpheno/bioconda_pcpheno.yaml @@ -4,7 +4,6 @@ description: Tools to integrate, annotate, and link phenotypes to cellular organ home: https://bioconductor.org/packages/3.10/bioc/html/PCpheno.html identifiers: - biotools:pcpheno -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-pcpheno summary: Phenotypes and cellular organizational units diff --git a/data/pepxmltab/bioconda_pepxmltab.yaml b/data/pepxmltab/bioconda_pepxmltab.yaml index f4f5a2c39dcd3..46d9602575e16 100644 --- a/data/pepxmltab/bioconda_pepxmltab.yaml +++ b/data/pepxmltab/bioconda_pepxmltab.yaml @@ -5,7 +5,6 @@ description: Parsing pepXML files based one XML package. The package tries to ha home: https://bioconductor.org/packages/3.10/bioc/html/pepXMLTab.html identifiers: - biotools:pepxmltab -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-pepxmltab summary: Parsing pepXML files and filter based on peptide FDR. diff --git a/data/pgsea/bioconda_pgsea.yaml b/data/pgsea/bioconda_pgsea.yaml index 4884a0fd07c4f..28ef6371374a9 100644 --- a/data/pgsea/bioconda_pgsea.yaml +++ b/data/pgsea/bioconda_pgsea.yaml @@ -3,7 +3,6 @@ description: Parametric Analysis of Gene Set Enrichment home: https://bioconductor.org/packages/3.10/bioc/html/PGSEA.html identifiers: - biotools:pgsea -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-pgsea diff --git a/data/pint/bioconda_pint.yaml b/data/pint/bioconda_pint.yaml index cd47f156c832a..97a21c98e5134 100644 --- a/data/pint/bioconda_pint.yaml +++ b/data/pint/bioconda_pint.yaml @@ -4,7 +4,6 @@ description: Pairwise data integration for functional genomics, including tools home: https://bioconductor.org/packages/3.10/bioc/html/pint.html identifiers: - biotools:pint -- doi:10.1038/nmeth.3252 license: BSD_2_clause + file LICENSE license_file: LICENSE name: bioconductor-pint diff --git a/data/pkgdeptools/bioconda_pkgdeptools.yaml b/data/pkgdeptools/bioconda_pkgdeptools.yaml index fed17016c183f..9d2f900e65fd5 100644 --- a/data/pkgdeptools/bioconda_pkgdeptools.yaml +++ b/data/pkgdeptools/bioconda_pkgdeptools.yaml @@ -8,7 +8,6 @@ description: This package provides tools for computing and analyzing dependency home: https://bioconductor.org/packages/3.10/bioc/html/pkgDepTools.html identifiers: - biotools:pkgdeptools -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-pkgdeptools diff --git a/data/plier/bioconda_plier.yaml b/data/plier/bioconda_plier.yaml index 5f595082f68a7..0b5db5fb3cc41 100644 --- a/data/plier/bioconda_plier.yaml +++ b/data/plier/bioconda_plier.yaml @@ -5,7 +5,6 @@ description: The PLIER (Probe Logarithmic Error Intensity Estimate) method produ home: https://bioconductor.org/packages/3.10/bioc/html/plier.html identifiers: - biotools:plier -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-plier diff --git a/data/plpe/bioconda_plpe.yaml b/data/plpe/bioconda_plpe.yaml index b264bc78a90d2..e82cbb41b7645 100644 --- a/data/plpe/bioconda_plpe.yaml +++ b/data/plpe/bioconda_plpe.yaml @@ -3,7 +3,6 @@ description: This package performs tests for paired high-throughput data. home: https://bioconductor.org/packages/3.10/bioc/html/PLPE.html identifiers: - biotools:plpe -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-plpe diff --git a/data/podkat/bioconda_podkat.yaml b/data/podkat/bioconda_podkat.yaml index 9d987a6b32464..084e2b8ccd364 100644 --- a/data/podkat/bioconda_podkat.yaml +++ b/data/podkat/bioconda_podkat.yaml @@ -9,7 +9,6 @@ description: This package provides an association test that is capable of dealin home: https://bioconductor.org/packages/3.10/bioc/html/podkat.html identifiers: - biotools:podkat -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-podkat diff --git a/data/prada/bioconda_prada.yaml b/data/prada/bioconda_prada.yaml index ff37d3e50219b..31e0a3a71b3b2 100644 --- a/data/prada/bioconda_prada.yaml +++ b/data/prada/bioconda_prada.yaml @@ -5,7 +5,6 @@ description: Tools for analysing and navigating data from high-throughput phenot home: https://bioconductor.org/packages/3.10/bioc/html/prada.html identifiers: - biotools:prada -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-prada diff --git a/data/preprocesscore/bioconda_preprocesscore.yaml b/data/preprocesscore/bioconda_preprocesscore.yaml index 333f73a81c5f6..a2ccb88922d8c 100644 --- a/data/preprocesscore/bioconda_preprocesscore.yaml +++ b/data/preprocesscore/bioconda_preprocesscore.yaml @@ -3,7 +3,6 @@ description: A library of core preprocessing routines. home: https://bioconductor.org/packages/3.10/bioc/html/preprocessCore.html identifiers: - biotools:preprocesscore -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-preprocesscore diff --git a/data/prize/bioconda_prize.yaml b/data/prize/bioconda_prize.yaml index 0cf6e892ea113..86320614fb58e 100644 --- a/data/prize/bioconda_prize.yaml +++ b/data/prize/bioconda_prize.yaml @@ -11,7 +11,6 @@ description: The high throughput studies often produce large amounts of numerous home: https://bioconductor.org/packages/3.10/bioc/html/Prize.html identifiers: - biotools:prize -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-prize summary: 'Prize: an R package for prioritization estimation based on analytic hierarchy diff --git a/data/process/bioconda_process.yaml b/data/process/bioconda_process.yaml index c2c9d9318176d..dcc0d9c61da24 100644 --- a/data/process/bioconda_process.yaml +++ b/data/process/bioconda_process.yaml @@ -3,7 +3,6 @@ description: A package for processing protein mass spectrometry data. home: https://bioconductor.org/packages/3.10/bioc/html/PROcess.html identifiers: - biotools:process -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-process summary: Ciphergen SELDI-TOF Processing diff --git a/data/profia/bioconda_profia.yaml b/data/profia/bioconda_profia.yaml index 6286675d2ac0c..8fea6de21eeb4 100644 --- a/data/profia/bioconda_profia.yaml +++ b/data/profia/bioconda_profia.yaml @@ -12,7 +12,6 @@ description: Flow Injection Analysis coupled to High-Resolution Mass Spectrometr home: https://bioconductor.org/packages/3.10/bioc/html/proFIA.html identifiers: - biotools:profia -- doi:10.1038/nmeth.3252 license: CeCILL name: bioconductor-profia summary: Preprocessing of FIA-HRMS data diff --git a/data/proteomicsannotationhubdata/bioconda_proteomicsannotationhubdata.yaml b/data/proteomicsannotationhubdata/bioconda_proteomicsannotationhubdata.yaml index 1bd9971c22ee1..7eebe2cc5ece0 100644 --- a/data/proteomicsannotationhubdata/bioconda_proteomicsannotationhubdata.yaml +++ b/data/proteomicsannotationhubdata/bioconda_proteomicsannotationhubdata.yaml @@ -4,7 +4,6 @@ description: These recipes convert a variety and a growing number of public prot home: https://bioconductor.org/packages/3.10/bioc/html/ProteomicsAnnotationHubData.html identifiers: - biotools:proteomicsannotationhubdata -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-proteomicsannotationhubdata summary: Transform public proteomics data resources into Bioconductor Data Structures diff --git a/data/protgenerics/bioconda_protgenerics.yaml b/data/protgenerics/bioconda_protgenerics.yaml index 515a06e241ee3..75927f781e35a 100644 --- a/data/protgenerics/bioconda_protgenerics.yaml +++ b/data/protgenerics/bioconda_protgenerics.yaml @@ -3,7 +3,6 @@ description: S4 generic functions needed by Bioconductor proteomics packages. home: https://bioconductor.org/packages/3.10/bioc/html/ProtGenerics.html identifiers: - biotools:protgenerics -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-protgenerics summary: S4 generic functions for Bioconductor proteomics infrastructure diff --git a/data/psicquic/bioconda_psicquic.yaml b/data/psicquic/bioconda_psicquic.yaml index 8c5e11a1edd58..5c4d2112a2c10 100644 --- a/data/psicquic/bioconda_psicquic.yaml +++ b/data/psicquic/bioconda_psicquic.yaml @@ -4,7 +4,6 @@ description: PSICQUIC is a project within the HUPO Proteomics Standard Initiativ home: https://bioconductor.org/packages/3.10/bioc/html/PSICQUIC.html identifiers: - biotools:psicquic -- doi:10.1038/nmeth.3252 license: Apache License 2.0 name: bioconductor-psicquic summary: Proteomics Standard Initiative Common QUery InterfaCe diff --git a/data/pwmenrich/bioconda_pwmenrich.yaml b/data/pwmenrich/bioconda_pwmenrich.yaml index 3d323788407ae..a2b7d53df2373 100644 --- a/data/pwmenrich/bioconda_pwmenrich.yaml +++ b/data/pwmenrich/bioconda_pwmenrich.yaml @@ -8,7 +8,6 @@ description: A toolkit of high-level functions for DNA motif scanning and enrich home: https://bioconductor.org/packages/3.10/bioc/html/PWMEnrich.html identifiers: - biotools:pwmenrich -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-pwmenrich diff --git a/data/qcmetrics/bioconda_qcmetrics.yaml b/data/qcmetrics/bioconda_qcmetrics.yaml index 444c2165c3711..9ec61baca262f 100644 --- a/data/qcmetrics/bioconda_qcmetrics.yaml +++ b/data/qcmetrics/bioconda_qcmetrics.yaml @@ -5,7 +5,6 @@ description: The package provides a framework for generic quality control of dat home: https://bioconductor.org/packages/3.10/bioc/html/qcmetrics.html identifiers: - biotools:qcmetrics -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-qcmetrics diff --git a/data/qrqc/bioconda_qrqc.yaml b/data/qrqc/bioconda_qrqc.yaml index 153da8cc51fd8..cab91f24cd816 100644 --- a/data/qrqc/bioconda_qrqc.yaml +++ b/data/qrqc/bioconda_qrqc.yaml @@ -7,7 +7,6 @@ description: Quickly scans reads and gathers statistics on base and quality freq home: https://bioconductor.org/packages/3.10/bioc/html/qrqc.html identifiers: - biotools:qrqc -- doi:10.1038/nmeth.3252 license: GPL (>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-qrqc diff --git a/data/quantsmooth/bioconda_quantsmooth.yaml b/data/quantsmooth/bioconda_quantsmooth.yaml index b110a354dd53c..64486efc0e899 100644 --- a/data/quantsmooth/bioconda_quantsmooth.yaml +++ b/data/quantsmooth/bioconda_quantsmooth.yaml @@ -4,7 +4,6 @@ description: 'Implements quantile smoothing as introduced in: Quantile smoothing home: https://bioconductor.org/packages/3.10/bioc/html/quantsmooth.html identifiers: - biotools:quantsmooth -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-quantsmooth diff --git a/data/randpack/bioconda_randpack.yaml b/data/randpack/bioconda_randpack.yaml index c75a31ac67905..9b1ff6cd894fd 100644 --- a/data/randpack/bioconda_randpack.yaml +++ b/data/randpack/bioconda_randpack.yaml @@ -4,7 +4,6 @@ description: A suite of classes and functions for randomizing patients in clinic home: https://bioconductor.org/packages/3.10/bioc/html/randPack.html identifiers: - biotools:randpack -- doi:10.1038/nmeth.3252 license: Artistic 2.0 name: bioconductor-randpack summary: Randomization routines for Clinical Trials diff --git a/data/rariant/bioconda_rariant.yaml b/data/rariant/bioconda_rariant.yaml index fb88b8902a294..f83583d2fb9c3 100644 --- a/data/rariant/bioconda_rariant.yaml +++ b/data/rariant/bioconda_rariant.yaml @@ -5,7 +5,6 @@ description: The 'Rariant' package identifies single nucleotide variants from se home: https://bioconductor.org/packages/3.10/bioc/html/Rariant.html identifiers: - biotools:rariant -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rariant diff --git a/data/rbcbook1/bioconda_rbcbook1.yaml b/data/rbcbook1/bioconda_rbcbook1.yaml index 2d309956069cd..77154c0550ed5 100644 --- a/data/rbcbook1/bioconda_rbcbook1.yaml +++ b/data/rbcbook1/bioconda_rbcbook1.yaml @@ -3,7 +3,6 @@ description: tools for building book home: https://bioconductor.org/packages/3.10/bioc/html/RbcBook1.html identifiers: - biotools:rbcbook1 -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-rbcbook1 summary: Support for Springer monograph on Bioconductor diff --git a/data/rbioinf/bioconda_rbioinf.yaml b/data/rbioinf/bioconda_rbioinf.yaml index bc5824a9dd528..8490753ce1aa1 100644 --- a/data/rbioinf/bioconda_rbioinf.yaml +++ b/data/rbioinf/bioconda_rbioinf.yaml @@ -4,7 +4,6 @@ description: Functions and datasets and examples to accompany the monograph R Fo home: https://bioconductor.org/packages/3.10/bioc/html/RBioinf.html identifiers: - biotools:rbioinf -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-rbioinf summary: RBioinf diff --git a/data/rbm/bioconda_rbm.yaml b/data/rbm/bioconda_rbm.yaml index fecf9bc15201b..63f77fed6db9a 100644 --- a/data/rbm/bioconda_rbm.yaml +++ b/data/rbm/bioconda_rbm.yaml @@ -4,7 +4,6 @@ description: Use A Resampling-Based Empirical Bayes Approach to Assess Different home: https://bioconductor.org/packages/3.10/bioc/html/RBM.html identifiers: - biotools:rbm -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rbm diff --git a/data/rbowtie/bioconda_rbowtie.yaml b/data/rbowtie/bioconda_rbowtie.yaml index d03afd11b7eff..c618fc32e33cf 100644 --- a/data/rbowtie/bioconda_rbowtie.yaml +++ b/data/rbowtie/bioconda_rbowtie.yaml @@ -6,7 +6,6 @@ description: This package provides an R wrapper around the popular bowtie short home: https://bioconductor.org/packages/3.10/bioc/html/Rbowtie.html identifiers: - biotools:rbowtie -- doi:10.1038/nmeth.3252 license: Artistic-2.0 | file LICENSE license_file: LICENSE name: bioconductor-rbowtie diff --git a/data/rcaspar/bioconda_rcaspar.yaml b/data/rcaspar/bioconda_rcaspar.yaml index 0333b30198555..dde9adafb1525 100644 --- a/data/rcaspar/bioconda_rcaspar.yaml +++ b/data/rcaspar/bioconda_rcaspar.yaml @@ -10,7 +10,6 @@ description: 'The package is the R-version of the C-based software \bold{CASPAR} home: https://bioconductor.org/packages/3.10/bioc/html/RCASPAR.html identifiers: - biotools:rcaspar -- doi:10.1038/nmeth.3252 license: GPL (>=3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rcaspar diff --git a/data/recoup/bioconda_recoup.yaml b/data/recoup/bioconda_recoup.yaml index ebef088f22b87..71aca8cbd3772 100644 --- a/data/recoup/bioconda_recoup.yaml +++ b/data/recoup/bioconda_recoup.yaml @@ -8,7 +8,6 @@ description: recoup calculates and plots signal profiles created from short sequ home: https://bioconductor.org/packages/3.10/bioc/html/recoup.html identifiers: - biotools:recoup -- doi:10.1038/nmeth.3252 license: GPL (>= 3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-recoup diff --git a/data/refnet/bioconda_refnet.yaml b/data/refnet/bioconda_refnet.yaml index 07bd2ff1454f9..8f7fc17b552d5 100644 --- a/data/refnet/bioconda_refnet.yaml +++ b/data/refnet/bioconda_refnet.yaml @@ -4,7 +4,6 @@ description: Obtain molecular interactions with metadata, some archived, some dy home: https://bioconductor.org/packages/3.10/bioc/html/RefNet.html identifiers: - biotools:refnet -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-refnet summary: A queryable collection of molecular interactions, from many sources diff --git a/data/regsplice/bioconda_regsplice.yaml b/data/regsplice/bioconda_regsplice.yaml index bf08c7af5f221..7e3f9c4cd3980 100644 --- a/data/regsplice/bioconda_regsplice.yaml +++ b/data/regsplice/bioconda_regsplice.yaml @@ -5,7 +5,6 @@ description: Statistical methods for detection of differential splicing (differe home: https://bioconductor.org/packages/3.10/bioc/html/regsplice.html identifiers: - biotools:regsplice -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-regsplice diff --git a/data/rgalaxy/bioconda_rgalaxy.yaml b/data/rgalaxy/bioconda_rgalaxy.yaml index df45c951d70a6..eab0512a3a7a5 100644 --- a/data/rgalaxy/bioconda_rgalaxy.yaml +++ b/data/rgalaxy/bioconda_rgalaxy.yaml @@ -4,7 +4,6 @@ description: Given an R function and its manual page, make the documented functi home: https://bioconductor.org/packages/3.10/bioc/html/RGalaxy.html identifiers: - biotools:rgalaxy -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-rgalaxy summary: Make an R function available in the Galaxy web platform diff --git a/data/rgraph2js/bioconda_rgraph2js.yaml b/data/rgraph2js/bioconda_rgraph2js.yaml index a5ed022c3077d..f20f5a80fae84 100644 --- a/data/rgraph2js/bioconda_rgraph2js.yaml +++ b/data/rgraph2js/bioconda_rgraph2js.yaml @@ -4,7 +4,6 @@ description: Generator of web pages which display interactive network/graph visu home: https://bioconductor.org/packages/3.10/bioc/html/RGraph2js.html identifiers: - biotools:rgraph2js -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-rgraph2js diff --git a/data/rgreat/bioconda_rgreat.yaml b/data/rgreat/bioconda_rgreat.yaml index 6ed0f80fa294e..a8047113ef28e 100644 --- a/data/rgreat/bioconda_rgreat.yaml +++ b/data/rgreat/bioconda_rgreat.yaml @@ -5,7 +5,6 @@ description: This package makes GREAT (Genomic Regions Enrichment of Annotations home: https://bioconductor.org/packages/3.10/bioc/html/rGREAT.html identifiers: - biotools:rgreat -- doi:10.1038/nmeth.3252 license: MIT + file LICENSE license_file: LICENSE name: bioconductor-rgreat diff --git a/data/rgsea/bioconda_rgsea.yaml b/data/rgsea/bioconda_rgsea.yaml index 8309e32e491a4..c67e0d178e53b 100644 --- a/data/rgsea/bioconda_rgsea.yaml +++ b/data/rgsea/bioconda_rgsea.yaml @@ -5,7 +5,6 @@ description: Combining bootstrap aggregating and Gene set enrichment analysis (G home: https://bioconductor.org/packages/3.10/bioc/html/RGSEA.html identifiers: - biotools:rgsea -- doi:10.1038/nmeth.3252 license: GPL(>=3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rgsea diff --git a/data/rgsepd/bioconda_rgsepd.yaml b/data/rgsepd/bioconda_rgsepd.yaml index 650219cefe4a7..84642eb82aa23 100644 --- a/data/rgsepd/bioconda_rgsepd.yaml +++ b/data/rgsepd/bioconda_rgsepd.yaml @@ -6,7 +6,6 @@ description: R/GSEPD is a bioinformatics package for R to help disambiguate tran home: https://bioconductor.org/packages/3.10/bioc/html/rgsepd.html identifiers: - biotools:rgsepd -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rgsepd diff --git a/data/rhtslib/bioconda_rhtslib.yaml b/data/rhtslib/bioconda_rhtslib.yaml index 3f3ed88d91844..34bbbe05bd780 100644 --- a/data/rhtslib/bioconda_rhtslib.yaml +++ b/data/rhtslib/bioconda_rhtslib.yaml @@ -6,7 +6,6 @@ description: This package provides version 1.7 of the 'HTSlib' C library for hig home: https://bioconductor.org/packages/3.10/bioc/html/Rhtslib.html identifiers: - biotools:rhtslib -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-rhtslib diff --git a/data/rmir/bioconda_rmir.yaml b/data/rmir/bioconda_rmir.yaml index 9d048609608ca..82a8a64c5c5a2 100644 --- a/data/rmir/bioconda_rmir.yaml +++ b/data/rmir/bioconda_rmir.yaml @@ -4,7 +4,6 @@ description: Useful functions to merge microRNA and respective targets using dif home: https://bioconductor.org/packages/3.10/bioc/html/RmiR.html identifiers: - biotools:rmir -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-rmir summary: Package to work with miRNAs and miRNA targets with R diff --git a/data/rnits/bioconda_rnits.yaml b/data/rnits/bioconda_rnits.yaml index c491aab9a91df..9c376fe82ca52 100644 --- a/data/rnits/bioconda_rnits.yaml +++ b/data/rnits/bioconda_rnits.yaml @@ -4,7 +4,6 @@ description: R/Bioconductor package for normalization, curve registration and in home: https://bioconductor.org/packages/3.10/bioc/html/Rnits.html identifiers: - biotools:rnits -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rnits diff --git a/data/roar/bioconda_roar.yaml b/data/roar/bioconda_roar.yaml index 1f1c48c472193..59c9c8d5c29d1 100644 --- a/data/roar/bioconda_roar.yaml +++ b/data/roar/bioconda_roar.yaml @@ -5,7 +5,6 @@ description: Identify preferential usage of APA sites, comparing two biological home: https://bioconductor.org/packages/3.10/bioc/html/roar.html identifiers: - biotools:roar -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-roar diff --git a/data/roc/bioconda_roc.yaml b/data/roc/bioconda_roc.yaml index 9f14685d37d66..04e668e750d4c 100644 --- a/data/roc/bioconda_roc.yaml +++ b/data/roc/bioconda_roc.yaml @@ -3,7 +3,6 @@ description: Provide utilities for ROC, with microarray focus. home: https://bioconductor.org/packages/3.10/bioc/html/ROC.html identifiers: - biotools:roc -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-roc summary: utilities for ROC, with microarray focus diff --git a/data/rols/bioconda_rols.yaml b/data/rols/bioconda_rols.yaml index f4a449a95b005..6541e843fa85c 100644 --- a/data/rols/bioconda_rols.yaml +++ b/data/rols/bioconda_rols.yaml @@ -4,7 +4,6 @@ description: The rols package is an interface to the Ontology Lookup Service (OL home: https://bioconductor.org/packages/3.10/bioc/html/rols.html identifiers: - biotools:rols -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-rols diff --git a/data/rrdp/bioconda_rrdp.yaml b/data/rrdp/bioconda_rrdp.yaml index 04cb8d1a838e7..256b653fcc4a2 100644 --- a/data/rrdp/bioconda_rrdp.yaml +++ b/data/rrdp/bioconda_rrdp.yaml @@ -3,7 +3,6 @@ description: Seamlessly interfaces RDP classifier (version 2.9). home: https://bioconductor.org/packages/3.10/bioc/html/rRDP.html identifiers: - biotools:rrdp -- doi:10.1038/nmeth.3252 license: GPL-2 | file LICENSE license_file: LICENSE name: bioconductor-rrdp diff --git a/data/rrho/bioconda_rrho.yaml b/data/rrho/bioconda_rrho.yaml index 1cd76fdf1de8c..3c5098c267c60 100644 --- a/data/rrho/bioconda_rrho.yaml +++ b/data/rrho/bioconda_rrho.yaml @@ -4,7 +4,6 @@ description: The package is aimed at inference on the amount of agreement in two home: https://bioconductor.org/packages/3.10/bioc/html/RRHO.html identifiers: - biotools:rrho -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-rrho diff --git a/data/rsamtools/bioconda_rsamtools.yaml b/data/rsamtools/bioconda_rsamtools.yaml index a49e39fb5007a..411c491120b17 100644 --- a/data/rsamtools/bioconda_rsamtools.yaml +++ b/data/rsamtools/bioconda_rsamtools.yaml @@ -5,7 +5,6 @@ description: This package provides an interface to the 'samtools', 'bcftools', a home: https://bioconductor.org/packages/3.10/bioc/html/Rsamtools.html identifiers: - biotools:rsamtools -- doi:10.1038/nmeth.3252 license: Artistic-2.0 | file LICENSE license_file: LICENSE name: bioconductor-rsamtools diff --git a/data/rtcga/bioconda_rtcga.yaml b/data/rtcga/bioconda_rtcga.yaml index 9f7b40c2fcb01..4f41d4a856cc5 100644 --- a/data/rtcga/bioconda_rtcga.yaml +++ b/data/rtcga/bioconda_rtcga.yaml @@ -11,7 +11,6 @@ description: The Cancer Genome Atlas (TCGA) Data Portal provides a platform for home: https://bioconductor.org/packages/3.10/bioc/html/RTCGA.html identifiers: - biotools:rtcga -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-rtcga diff --git a/data/rtrmui/bioconda_rtrmui.yaml b/data/rtrmui/bioconda_rtrmui.yaml index e0a4b19cb5d56..9c3a20987b614 100644 --- a/data/rtrmui/bioconda_rtrmui.yaml +++ b/data/rtrmui/bioconda_rtrmui.yaml @@ -4,7 +4,6 @@ description: This package provides a web interface to compute transcriptional re home: https://bioconductor.org/packages/3.10/bioc/html/rTRMui.html identifiers: - biotools:rtrmui -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-rtrmui diff --git a/data/s4vectors/bioconda_s4vectors.yaml b/data/s4vectors/bioconda_s4vectors.yaml index 0e9d9d5ceb3cb..2f16d72645396 100644 --- a/data/s4vectors/bioconda_s4vectors.yaml +++ b/data/s4vectors/bioconda_s4vectors.yaml @@ -9,7 +9,6 @@ description: The S4Vectors package defines the Vector and List virtual classes a home: https://bioconductor.org/packages/3.10/bioc/html/S4Vectors.html identifiers: - biotools:s4vectors -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-s4vectors summary: Foundation of vector-like and list-like containers in Bioconductor diff --git a/data/sagenhaft/bioconda_sagenhaft.yaml b/data/sagenhaft/bioconda_sagenhaft.yaml index c6d33afea8e77..4045acc69307e 100644 --- a/data/sagenhaft/bioconda_sagenhaft.yaml +++ b/data/sagenhaft/bioconda_sagenhaft.yaml @@ -7,7 +7,6 @@ description: This package implements several functions useful for analysis of ge home: https://bioconductor.org/packages/3.10/bioc/html/sagenhaft.html identifiers: - biotools:sagenhaft -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-sagenhaft diff --git a/data/sagx/bioconda_sagx.yaml b/data/sagx/bioconda_sagx.yaml index 05728146b857b..34e8c0b895977 100644 --- a/data/sagx/bioconda_sagx.yaml +++ b/data/sagx/bioconda_sagx.yaml @@ -5,7 +5,6 @@ description: A package for retrieval, preparation and analysis of data from the home: https://bioconductor.org/packages/3.10/bioc/html/SAGx.html identifiers: - biotools:sagx -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-sagx diff --git a/data/savr/bioconda_savr.yaml b/data/savr/bioconda_savr.yaml index 3a88e059bb2b7..de30c49f41ecd 100644 --- a/data/savr/bioconda_savr.yaml +++ b/data/savr/bioconda_savr.yaml @@ -4,7 +4,6 @@ description: Parse Illumina Sequence Analysis Viewer (SAV) files, access data, a home: https://bioconductor.org/packages/3.10/bioc/html/savR.html identifiers: - biotools:savr -- doi:10.1038/nmeth.3252 license: AGPL-3 license_file: /lib/R/share/licenses/AGPL-3 name: bioconductor-savr diff --git a/data/scisi/bioconda_scisi.yaml b/data/scisi/bioconda_scisi.yaml index e94dbb327d9ee..8f40ae83ffc7e 100644 --- a/data/scisi/bioconda_scisi.yaml +++ b/data/scisi/bioconda_scisi.yaml @@ -3,7 +3,6 @@ description: Package to create In Silico Interactomes home: https://bioconductor.org/packages/3.10/bioc/html/ScISI.html identifiers: - biotools:scisi -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-scisi diff --git a/data/semdist/bioconda_semdist.yaml b/data/semdist/bioconda_semdist.yaml index ff99139e514ac..0b396049c1be0 100644 --- a/data/semdist/bioconda_semdist.yaml +++ b/data/semdist/bioconda_semdist.yaml @@ -6,7 +6,6 @@ description: This package implements methods to calculate information accretion home: https://bioconductor.org/packages/3.10/bioc/html/SemDist.html identifiers: - biotools:semdist -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-semdist diff --git a/data/sepa/bioconda_sepa.yaml b/data/sepa/bioconda_sepa.yaml index 8c30c1cb1e5cd..9d47d54475c5c 100644 --- a/data/sepa/bioconda_sepa.yaml +++ b/data/sepa/bioconda_sepa.yaml @@ -2,7 +2,6 @@ biotools_id: sepa home: https://bioconductor.org/packages/3.9/bioc/html/SEPA.html identifiers: - biotools:sepa -- doi:10.1038/nmeth.3252 license: GPL(>=2) name: bioconductor-sepa summary: Given single-cell RNA-seq data and true experiment time of cells or pseudo-time diff --git a/data/seqlogo/bioconda_seqlogo.yaml b/data/seqlogo/bioconda_seqlogo.yaml index f21984e193c6e..99f2c5f8b051f 100644 --- a/data/seqlogo/bioconda_seqlogo.yaml +++ b/data/seqlogo/bioconda_seqlogo.yaml @@ -4,7 +4,6 @@ description: seqLogo takes the position weight matrix of a DNA sequence motif an home: https://bioconductor.org/packages/3.10/bioc/html/seqLogo.html identifiers: - biotools:seqlogo -- doi:10.1038/nmeth.3252 license: LGPL (>= 2) license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-seqlogo diff --git a/data/seqpattern/bioconda_seqpattern.yaml b/data/seqpattern/bioconda_seqpattern.yaml index 2f975c5b12e3b..18cfed960957e 100644 --- a/data/seqpattern/bioconda_seqpattern.yaml +++ b/data/seqpattern/bioconda_seqpattern.yaml @@ -5,7 +5,6 @@ description: Visualising oligonucleotide patterns and sequence motifs occurrence home: https://bioconductor.org/packages/3.10/bioc/html/seqPattern.html identifiers: - biotools:seqpattern -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-seqpattern diff --git a/data/seqtools/bioconda_seqtools.yaml b/data/seqtools/bioconda_seqtools.yaml index 97b736314c5da..ed91f60298439 100644 --- a/data/seqtools/bioconda_seqtools.yaml +++ b/data/seqtools/bioconda_seqtools.yaml @@ -4,7 +4,6 @@ description: Analyze read length, phred scores and alphabet frequency and DNA k- home: https://bioconductor.org/packages/3.10/bioc/html/seqTools.html identifiers: - biotools:seqtools -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-seqtools summary: Analysis of nucleotide, sequence and quality content on fastq files diff --git a/data/sigar/bioconda_sigar.yaml b/data/sigar/bioconda_sigar.yaml index d708fde122784..554f1805b0783 100644 --- a/data/sigar/bioconda_sigar.yaml +++ b/data/sigar/bioconda_sigar.yaml @@ -5,7 +5,6 @@ description: Facilitates the joint analysis of high-throughput data from multipl home: https://bioconductor.org/packages/3.10/bioc/html/sigaR.html identifiers: - biotools:sigar -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-sigar diff --git a/data/sigpathway/bioconda_sigpathway.yaml b/data/sigpathway/bioconda_sigpathway.yaml index e4a5df9afa87a..7cde1e4b925a3 100644 --- a/data/sigpathway/bioconda_sigpathway.yaml +++ b/data/sigpathway/bioconda_sigpathway.yaml @@ -4,7 +4,6 @@ description: Conducts pathway analysis by calculating the NT_k and NE_k statisti home: https://bioconductor.org/packages/3.10/bioc/html/sigPathway.html identifiers: - biotools:sigpathway -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-sigpathway diff --git a/data/simbindprofiles/bioconda_simbindprofiles.yaml b/data/simbindprofiles/bioconda_simbindprofiles.yaml index 6ac40c2030725..185f1c8314d5d 100644 --- a/data/simbindprofiles/bioconda_simbindprofiles.yaml +++ b/data/simbindprofiles/bioconda_simbindprofiles.yaml @@ -7,7 +7,6 @@ description: SimBindProfiles identifies common and unique binding regions in gen home: https://bioconductor.org/packages/3.10/bioc/html/SimBindProfiles.html identifiers: - biotools:simbindprofiles -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-simbindprofiles diff --git a/data/sizepower/bioconda_sizepower.yaml b/data/sizepower/bioconda_sizepower.yaml index 1443425b5012b..0869c3af96b62 100644 --- a/data/sizepower/bioconda_sizepower.yaml +++ b/data/sizepower/bioconda_sizepower.yaml @@ -8,7 +8,6 @@ description: This package has been prepared to assist users in computing either home: https://bioconductor.org/packages/3.10/bioc/html/sizepower.html identifiers: - biotools:sizepower -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-sizepower diff --git a/data/slqpcr/bioconda_slqpcr.yaml b/data/slqpcr/bioconda_slqpcr.yaml index d8a9b6e318642..f97c7d4deef79 100644 --- a/data/slqpcr/bioconda_slqpcr.yaml +++ b/data/slqpcr/bioconda_slqpcr.yaml @@ -4,7 +4,6 @@ description: Functions for analysis of real-time quantitative PCR data at SIRS-L home: https://bioconductor.org/packages/3.10/bioc/html/SLqPCR.html identifiers: - biotools:slqpcr -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-slqpcr diff --git a/data/snpstats/bioconda_snpstats.yaml b/data/snpstats/bioconda_snpstats.yaml index 7d86241674da8..53d1c8a92180a 100644 --- a/data/snpstats/bioconda_snpstats.yaml +++ b/data/snpstats/bioconda_snpstats.yaml @@ -4,7 +4,6 @@ description: Classes and statistical methods for large SNP association studies. home: https://bioconductor.org/packages/3.10/bioc/html/snpStats.html identifiers: - biotools:snpstats -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-snpstats diff --git a/data/soggi/bioconda_soggi.yaml b/data/soggi/bioconda_soggi.yaml index 547b3ef3e9c8f..85b39e4908d77 100644 --- a/data/soggi/bioconda_soggi.yaml +++ b/data/soggi/bioconda_soggi.yaml @@ -11,7 +11,6 @@ description: The soGGi package provides a toolset to create genomic interval agg home: https://bioconductor.org/packages/3.10/bioc/html/soGGi.html identifiers: - biotools:soggi -- doi:10.1038/nmeth.3252 license: GPL (>= 3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-soggi diff --git a/data/spikeli/bioconda_spikeli.yaml b/data/spikeli/bioconda_spikeli.yaml index d17c694e98377..f0037c8f9096a 100644 --- a/data/spikeli/bioconda_spikeli.yaml +++ b/data/spikeli/bioconda_spikeli.yaml @@ -9,7 +9,6 @@ description: SpikeLI is a package that performs the analysis of the Affymetrix s home: https://bioconductor.org/packages/3.10/bioc/html/spikeLI.html identifiers: - biotools:spikeli -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-spikeli diff --git a/data/splicegear/bioconda_splicegear.yaml b/data/splicegear/bioconda_splicegear.yaml index bed53ca0ab719..2a13c8ccea49e 100644 --- a/data/splicegear/bioconda_splicegear.yaml +++ b/data/splicegear/bioconda_splicegear.yaml @@ -3,7 +3,6 @@ description: A set of tools to work with alternative splicing home: https://bioconductor.org/packages/3.10/bioc/html/splicegear.html identifiers: - biotools:splicegear -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-splicegear diff --git a/data/splinter/bioconda_splinter.yaml b/data/splinter/bioconda_splinter.yaml index 2674152247232..4298ae6195c17 100644 --- a/data/splinter/bioconda_splinter.yaml +++ b/data/splinter/bioconda_splinter.yaml @@ -5,7 +5,6 @@ description: Provides tools to analyze alternative splicing sites, interpret out home: https://bioconductor.org/packages/3.10/bioc/html/SPLINTER.html identifiers: - biotools:splinter -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-splinter diff --git a/data/splots/bioconda_splots.yaml b/data/splots/bioconda_splots.yaml index 95dd44869ead2..21866965dad99 100644 --- a/data/splots/bioconda_splots.yaml +++ b/data/splots/bioconda_splots.yaml @@ -4,7 +4,6 @@ description: The splots package provides the plotScreen function for visualising home: https://bioconductor.org/packages/3.10/bioc/html/splots.html identifiers: - biotools:splots -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-splots diff --git a/data/squadd/bioconda_squadd.yaml b/data/squadd/bioconda_squadd.yaml index 7d9ee059dd244..403638cdd8010 100644 --- a/data/squadd/bioconda_squadd.yaml +++ b/data/squadd/bioconda_squadd.yaml @@ -4,7 +4,6 @@ description: This package SQUADD is a SQUAD add-on. It permits to generate SQUAD home: https://bioconductor.org/packages/3.10/bioc/html/SQUADD.html identifiers: - biotools:squadd -- doi:10.1038/nmeth.3252 license: GPL (>=2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-squadd diff --git a/data/sscu/bioconda_sscu.yaml b/data/sscu/bioconda_sscu.yaml index 65062dbc91853..13fa80fa2c462 100644 --- a/data/sscu/bioconda_sscu.yaml +++ b/data/sscu/bioconda_sscu.yaml @@ -20,7 +20,6 @@ description: The package calculates the indexes for selective stength in codon u home: https://bioconductor.org/packages/3.10/bioc/html/sscu.html identifiers: - biotools:sscu -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-sscu diff --git a/data/ssize/bioconda_ssize.yaml b/data/ssize/bioconda_ssize.yaml index c335d17a1d3e6..6f7535b27678f 100644 --- a/data/ssize/bioconda_ssize.yaml +++ b/data/ssize/bioconda_ssize.yaml @@ -4,7 +4,6 @@ description: Functions for computing and displaying sample size information for home: https://bioconductor.org/packages/3.10/bioc/html/ssize.html identifiers: - biotools:ssize -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-ssize diff --git a/data/ssviz/bioconda_ssviz.yaml b/data/ssviz/bioconda_ssviz.yaml index 6064ce615f664..8e85f19a69b53 100644 --- a/data/ssviz/bioconda_ssviz.yaml +++ b/data/ssviz/bioconda_ssviz.yaml @@ -3,7 +3,6 @@ description: Small RNA sequencing viewer home: https://bioconductor.org/packages/3.10/bioc/html/ssviz.html identifiers: - biotools:ssviz -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-ssviz diff --git a/data/streamer/bioconda_streamer.yaml b/data/streamer/bioconda_streamer.yaml index e63efe1055e0d..876ae08e052a2 100644 --- a/data/streamer/bioconda_streamer.yaml +++ b/data/streamer/bioconda_streamer.yaml @@ -8,7 +8,6 @@ description: Large data files can be difficult to work with in R, where data gen home: https://bioconductor.org/packages/3.10/bioc/html/Streamer.html identifiers: - biotools:streamer -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-streamer summary: Enabling stream processing of large files diff --git a/data/summarizedexperiment/bioconda_summarizedexperiment.yaml b/data/summarizedexperiment/bioconda_summarizedexperiment.yaml index 5626946b8cd4f..17d9db08efdcc 100644 --- a/data/summarizedexperiment/bioconda_summarizedexperiment.yaml +++ b/data/summarizedexperiment/bioconda_summarizedexperiment.yaml @@ -5,7 +5,6 @@ description: The SummarizedExperiment container contains one or more assays, eac home: https://bioconductor.org/packages/3.10/bioc/html/SummarizedExperiment.html identifiers: - biotools:summarizedexperiment -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-summarizedexperiment summary: SummarizedExperiment container diff --git a/data/timecourse/bioconda_timecourse.yaml b/data/timecourse/bioconda_timecourse.yaml index c2e607b271642..16252ad1f18cb 100644 --- a/data/timecourse/bioconda_timecourse.yaml +++ b/data/timecourse/bioconda_timecourse.yaml @@ -4,7 +4,6 @@ description: Functions for data analysis and graphical displays for developmenta home: https://bioconductor.org/packages/3.10/bioc/html/timecourse.html identifiers: - biotools:timecourse -- doi:10.1038/nmeth.3252 license: LGPL license_file: /lib/R/share/licenses/LGPL-3 name: bioconductor-timecourse diff --git a/data/tracktables/bioconda_tracktables.yaml b/data/tracktables/bioconda_tracktables.yaml index fe776c312fd58..9e405653ab726 100644 --- a/data/tracktables/bioconda_tracktables.yaml +++ b/data/tracktables/bioconda_tracktables.yaml @@ -4,7 +4,6 @@ description: Methods to create complex IGV genome browser sessions and dynamic I home: https://bioconductor.org/packages/3.10/bioc/html/tracktables.html identifiers: - biotools:tracktables -- doi:10.1038/nmeth.3252 license: GPL (>= 3) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-tracktables diff --git a/data/trackviewer/bioconda_trackviewer.yaml b/data/trackviewer/bioconda_trackviewer.yaml index e277307b9c586..4e36d8f3d0c7c 100644 --- a/data/trackviewer/bioconda_trackviewer.yaml +++ b/data/trackviewer/bioconda_trackviewer.yaml @@ -4,7 +4,6 @@ description: Visualize mapped reads along with annotation as track layers for NG home: https://bioconductor.org/packages/3.10/bioc/html/trackViewer.html identifiers: - biotools:trackviewer -- doi:10.1038/nmeth.3252 license: GPL (>= 2) license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-trackviewer diff --git a/data/transcriptr/bioconda_transcriptr.yaml b/data/transcriptr/bioconda_transcriptr.yaml index 53271ad97026c..93c8de7d57848 100644 --- a/data/transcriptr/bioconda_transcriptr.yaml +++ b/data/transcriptr/bioconda_transcriptr.yaml @@ -19,7 +19,6 @@ description: The differences in the RNA types being sequenced have an impact on home: https://bioconductor.org/packages/3.10/bioc/html/transcriptR.html identifiers: - biotools:transcriptr -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-transcriptr diff --git a/data/transview/bioconda_transview.yaml b/data/transview/bioconda_transview.yaml index 12adcaef1e62d..3cb2121808bb3 100644 --- a/data/transview/bioconda_transview.yaml +++ b/data/transview/bioconda_transview.yaml @@ -4,7 +4,6 @@ description: This package provides efficient tools to generate, access and displ home: https://bioconductor.org/packages/3.10/bioc/html/TransView.html identifiers: - biotools:transview -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-transview diff --git a/data/trigger/bioconda_trigger.yaml b/data/trigger/bioconda_trigger.yaml index d824f280d73ac..401d103bb4eb3 100644 --- a/data/trigger/bioconda_trigger.yaml +++ b/data/trigger/bioconda_trigger.yaml @@ -11,7 +11,6 @@ description: 'This R package provides tools for the statistical analysis of inte home: https://bioconductor.org/packages/3.10/bioc/html/trigger.html identifiers: - biotools:trigger -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-trigger diff --git a/data/trio/bioconda_trio.yaml b/data/trio/bioconda_trio.yaml index 871ed661e2d75..bafb9f6933c31 100644 --- a/data/trio/bioconda_trio.yaml +++ b/data/trio/bioconda_trio.yaml @@ -8,7 +8,6 @@ description: Testing SNPs and SNP interactions with a genotypic TDT. This packag home: https://bioconductor.org/packages/3.10/bioc/html/trio.html identifiers: - biotools:trio -- doi:10.1038/nmeth.3252 license: LGPL-2 license_file: /lib/R/share/licenses/LGPL-2 name: bioconductor-trio diff --git a/data/tvtb/bioconda_tvtb.yaml b/data/tvtb/bioconda_tvtb.yaml index 5967c82876dc5..9eb60d4823054 100644 --- a/data/tvtb/bioconda_tvtb.yaml +++ b/data/tvtb/bioconda_tvtb.yaml @@ -7,7 +7,6 @@ description: The package provides S4 classes and methods to filter, summarise an home: https://bioconductor.org/packages/3.10/bioc/html/TVTB.html identifiers: - biotools:tvtb -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-tvtb summary: 'TVTB: The VCF Tool Box' diff --git a/data/uniprot.ws/bioconda_uniprot.ws.yaml b/data/uniprot.ws/bioconda_uniprot.ws.yaml index b93ab4c90b09a..ac64e3697bf68 100644 --- a/data/uniprot.ws/bioconda_uniprot.ws.yaml +++ b/data/uniprot.ws/bioconda_uniprot.ws.yaml @@ -4,7 +4,6 @@ description: A collection of functions for retrieving, processing and repackagin home: https://bioconductor.org/packages/3.10/bioc/html/UniProt.ws.html identifiers: - biotools:uniprot.ws -- doi:10.1038/nmeth.3252 license: Artistic License 2.0 name: bioconductor-uniprot.ws summary: R Interface to UniProt Web Services diff --git a/data/variantfiltering/bioconda_variantfiltering.yaml b/data/variantfiltering/bioconda_variantfiltering.yaml index 23ded52c7bb4c..78942f229dc4d 100644 --- a/data/variantfiltering/bioconda_variantfiltering.yaml +++ b/data/variantfiltering/bioconda_variantfiltering.yaml @@ -5,7 +5,6 @@ description: Filter genetic variants using different criteria such as inheritanc home: https://bioconductor.org/packages/3.10/bioc/html/VariantFiltering.html identifiers: - biotools:variantfiltering -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-variantfiltering summary: Filtering of coding and non-coding genetic variants diff --git a/data/weaver/bioconda_weaver.yaml b/data/weaver/bioconda_weaver.yaml index 2a939d85d28b9..cfc86119a3f5d 100644 --- a/data/weaver/bioconda_weaver.yaml +++ b/data/weaver/bioconda_weaver.yaml @@ -4,7 +4,6 @@ description: This package provides enhancements on the Sweave() function in the home: https://bioconductor.org/packages/3.10/bioc/html/weaver.html identifiers: - biotools:weaver -- doi:10.1038/nmeth.3252 license: GPL-2 license_file: /lib/R/share/licenses/GPL-2 name: bioconductor-weaver diff --git a/data/xvector/bioconda_xvector.yaml b/data/xvector/bioconda_xvector.yaml index 7c4b734feae6e..e4c82799b2d82 100644 --- a/data/xvector/bioconda_xvector.yaml +++ b/data/xvector/bioconda_xvector.yaml @@ -4,7 +4,6 @@ description: Provides memory efficient S4 classes for storing sequences "externa home: https://bioconductor.org/packages/3.10/bioc/html/XVector.html identifiers: - biotools:xvector -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-xvector summary: Foundation of external vector representation and manipulation in Bioconductor diff --git a/data/yapsa/bioconda_yapsa.yaml b/data/yapsa/bioconda_yapsa.yaml index a78230e4148d7..17e50c69df9f9 100644 --- a/data/yapsa/bioconda_yapsa.yaml +++ b/data/yapsa/bioconda_yapsa.yaml @@ -7,7 +7,6 @@ description: This package provides functions and routines useful in the analysis home: https://bioconductor.org/packages/3.10/bioc/html/YAPSA.html identifiers: - biotools:yapsa -- doi:10.1038/nmeth.3252 license: GPL-3 license_file: /lib/R/share/licenses/GPL-3 name: bioconductor-yapsa diff --git a/data/yaqcaffy/bioconda_yaqcaffy.yaml b/data/yaqcaffy/bioconda_yaqcaffy.yaml index 2b4f570e5e25c..b64027a793a72 100644 --- a/data/yaqcaffy/bioconda_yaqcaffy.yaml +++ b/data/yaqcaffy/bioconda_yaqcaffy.yaml @@ -4,7 +4,6 @@ description: Quality control of Affymetrix GeneChip expression data and reproduc home: https://bioconductor.org/packages/3.10/bioc/html/yaqcaffy.html identifiers: - biotools:yaqcaffy -- doi:10.1038/nmeth.3252 license: Artistic-2.0 name: bioconductor-yaqcaffy summary: Affymetrix expression data quality control and reproducibility analysis diff --git a/data/zlibbioc/bioconda_zlibbioc.yaml b/data/zlibbioc/bioconda_zlibbioc.yaml index 433b88d5c0e3d..06e74d4d88b60 100644 --- a/data/zlibbioc/bioconda_zlibbioc.yaml +++ b/data/zlibbioc/bioconda_zlibbioc.yaml @@ -6,7 +6,6 @@ description: This package uses the source code of zlib-1.2.5 to create libraries home: https://bioconductor.org/packages/3.10/bioc/html/zlibbioc.html identifiers: - biotools:zlibbioc -- doi:10.1038/nmeth.3252 license: Artistic-2.0 + file LICENSE license_file: LICENSE name: bioconductor-zlibbioc