CNR-IBBA

All

26 repositories

nf-resequencing-mem
Public
Nextflow resequencing pipeline with bwa-mem and freebayes
nextflow bwa-mem bcftools resequencing freebayes nextflow-pipeline nextflow-dsl2
Nextflow
•
MIT License
•0•0•8•1•Updated Jan 14, 2025Jan 14, 2025
nf-configs
Public
Config files used to define parameters specific to compute environments at different Institutions
Nextflow
•
MIT License
•281•0•0•0•Updated Jan 14, 2025Jan 14, 2025
BIOINFO-guidelines
Public
Bioinformatic Guidelines @ IBBA-CNR
GNU General Public License v3.0
•1•3•2•1•Updated Nov 7, 2024Nov 7, 2024
SMARTER-database
Public
Smarter database repository
database efficiency plink breeding genotype smarter resilience affymetrix ruminant
Jupyter Notebook
•
MIT License
•0•1•10•3•Updated Oct 16, 2024Oct 16, 2024
SMARTER-frontend
Public
SMARTER Database frontend
frontend smarter angular
TypeScript
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MIT License
•0•0•5•11•Updated Oct 8, 2024Oct 8, 2024
nf-treeseq
Public
Nextflow pipeline to convert genotype data into Tree Sequences
nextflow tskit treeseq
Nextflow
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MIT License
•0•0•7•0•Updated Sep 5, 2024Sep 5, 2024
SMARTER-backend
Public
SMARTER Backend API
flask rest-api mongoengine smarter flask-restful flask-mongoengine
Python
•
GNU General Public License v3.0
•0•0•7•4•Updated Sep 3, 2024Sep 3, 2024
SMARTER-repository
Public
SMARTER Data Repository
data repository smarter bootstrap5 django
Python
•0•0•2•0•Updated Jul 1, 2024Jul 1, 2024
r-smarter-api
Public
R code to query SMARTER-backend
smarter api
R
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GNU General Public License v3.0
•0•2•2•0•Updated Jun 28, 2024Jun 28, 2024
nf-chip-alignment
Public
Align chip probes to a reference genome
manifest genome alignment chip blat smarter snpchimp
Python
•
MIT License
•0•1•3•0•Updated May 2, 2024May 2, 2024
dockerfiles
Public
A useful repository for Docker file
Perl
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GNU General Public License v3.0
•1•4•0•1•Updated Apr 15, 2024Apr 15, 2024
nf-modules
Public
Custom Nextflow DSL2 modules
modules nextflow dsl2 nextflow-modules
Nextflow
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MIT License
•0•0•4•1•Updated Mar 15, 2024Mar 15, 2024
nf-neestimator
Public
A nextflow pipeline for Current Effective Population Size (Ne) calculations with bootstrapping
bootstrap plink population size current effective nextflow-pipeline dsl2 pgdspider2 neestimator
Nextflow
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MIT License
•0•0•1•0•Updated Mar 4, 2024Mar 4, 2024
nf-treemix
Public
A nextflow pipeline which executes treemix on a population of interest
nextflow consensus phylip nextflow-pipeline treemix orientagraph optm
Nextflow
•0•1•2•0•Updated Aug 3, 2023Aug 3, 2023
IMAGE-InjectTool
Public
Load IMAGE data into BioSample
Python
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GNU General Public License v3.0
•0•3•7•1•Updated Jun 12, 2023Jun 12, 2023
pyUSIrest
Public
Python USI submission REST API contain all methods to interact with EMBL-EBI Unified Submissions Interface
Python
•
Other
•0•1•1•2•Updated Dec 26, 2022Dec 26, 2022
IMAGE-CommonDataPool
Public
IMAGE Common Data Pool - PostgreSQL, metadata structure and data loading scripts
Python
•
Apache License 2.0
•0•0•2•0•Updated Apr 1, 2022Apr 1, 2022
shiny-server
Public
Shiny Server @cnr-ibba
docker docker-compose shiny-server django-authentication
JavaScript
•
GNU General Public License v3.0
•2•7•1•1•Updated Oct 20, 2021Oct 20, 2021
IMAGE-ValidationTool
Public
IMAGE Validation Tool component of the IMAGE Inject Tool
Python
•
Apache License 2.0
•0•0•1•1•Updated Jun 9, 2021Jun 9, 2021
IMAGE-Portal
Public
IMAGE Data Portal - Frontend code for IMAGE Data Portal and API
TypeScript
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Apache License 2.0
•0•0•0•8•Updated May 12, 2021May 12, 2021
IMAGE-ansible
Public
Ansible configuration for image server
Jinja
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GNU General Public License v3.0
•0•0•0•0•Updated May 11, 2021May 11, 2021
IMAGE-DiversityBrowser
Public
Manage code for IMAGE Diversity Browser
Jupyter Notebook
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Apache License 2.0
•0•0•0•0•Updated Mar 3, 2020Mar 3, 2020
IMAGE-genotype
Public
EVA submission guideline and the import script
Python
•0•0•0•0•Updated Jan 29, 2020Jan 29, 2020
IMAGE-metadata
Public
IMAGE metadata definitions
Perl
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Apache License 2.0
•0•0•0•0•Updated Oct 2, 2019Oct 2, 2019
svevo-hapflk
Public
Hapflk analysis of durum wheat
R
•0•0•0•0•Updated Aug 23, 2018Aug 23, 2018
svevo-permutations
Public
Permutations for Fst calculations in durum wheat genetics
R
•0•0•0•0•Updated Aug 23, 2018Aug 23, 2018