Repositories list

• h3k4me3_maintenance

  Public
  HTML

  •0•0•0•0•Updated Jan 14, 2025Jan 14, 2025

• scXen

  Public
  Analysis of scRNA-seq data from nuclear transfer Xenopus embryos

  Jupyter Notebook

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• STREAMLINE

  Public
  STREAMLINE (Topological benchmarking of GRN inference from scRNA-Sequencing data)

  HTML

  •0•5•0•0•Updated Jun 6, 2024Jun 6, 2024

• scAVE

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Mar 18, 2024Mar 18, 2024

• Reprogramming-cell-fate---Ding-Yang

  Public
  The code and data that used in the intern. The aim of the internship is to find whether the boundaries in blastula cells change after nucleus transfer.

  0•0•0•0•Updated Nov 9, 2023Nov 9, 2023

• MATACseq

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 18, 2023Oct 18, 2023

• CIARA

  Public
  CIARA (Cluster Independent Algorithm for the identification of markers of RAre cell types) is an R package that identifies potential markers of rare cell types looking at genes whose expression is confined in small regions of the expression space

  open-sourcefeature-selectioncluster-analysis+ 3bioinformatics-analysisrstats-packagerare-cells

  R

  •2•15•1•0•Updated May 23, 2023May 23, 2023

• human-gastrula-shiny

  Public
  R

  •1•2•2•0•Updated Apr 3, 2023Apr 3, 2023

• CIARA_python

  Public
  Implementation of entropy of mixing algorithm in python

  opensourcebioinformaticsrna-seq+ 6feature-selectionrna-seq-analysisbioinformatics-analysisbioinformatics-algorithmsbioinformatics-toolcelltype-annotation

  Jupyter Notebook

  •

  MIT License

  •1•8•0•0•Updated Oct 19, 2022Oct 19, 2022

• WOTPLY

  Public
  R

  •1•1•0•0•Updated Oct 6, 2022Oct 6, 2022

• 2DLEGI

  Public
  Impact of size and geometry of 2D epithelial tissues on the precision of gradient sensing via nearest-neighbour or long-range intercellular communication

  Jupyter Notebook

  •0•1•0•0•Updated Jun 29, 2022Jun 29, 2022

• MitoHEAR

  Public
  MitoHEAR (Mitochondrial HEteroplasmy AnalyzeR) is an R package that allows the estimation as well as downstream statistical analysis of the mtDNA heteroplasmy calculated from single-cell datasets.

  open-sourcebioinformatics-analysisheteroplasmy+ 1rstats-package

  R

  •

  GNU General Public License v3.0

  •3•1•0•0•Updated Jun 2, 2022Jun 2, 2022

• scanpy

  Public
  Single-cell analysis in Python. Scales to >1M cells.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •616•0•0•0•Updated Mar 28, 2022Mar 28, 2022

• seurat-wrappers

  Public
  Community-provided extensions to Seurat

  R

  •

  GNU General Public License v3.0

  •135•0•0•0•Updated Mar 16, 2022Mar 16, 2022

• Spatial-Transcriptomics

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 11, 2022Feb 11, 2022

• gastrula_code

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Feb 3, 2022Feb 3, 2022

• GRANpy

  Public
  Graph Auto-Encoders (GAE) for Gene Regulatory Network (GRN) completion using scRNA-Seq datasets

  Python

  •

  MIT License

  •350•2•0•0•Updated Jan 19, 2022Jan 19, 2022

• DiffVAE

  Public
  Code for Nature Scientific Reports 2020 paper: "Unsupervised generative and graph neural methods for modelling cell differentiation" by Ioana Bica, Helena Andrés-Terré, Ana Cvejic, Pietro Liò

  Jupyter Notebook

  •

  MIT License

  •2•0•0•0•Updated Jul 9, 2021Jul 9, 2021

• Cell-Competition-Paper-Figures

  Public
  HTML

  •0•0•0•0•Updated Jul 2, 2021Jul 2, 2021

• COMUNET

  Public template
  COMUNET: a tool to explore and visualize intercellular communication

  Jupyter Notebook

  •10•12•2•0•Updated Apr 15, 2020Apr 15, 2020