Repositories list

• FastReadCounter

  Public
  Tool for fast counting of reads from BAM file into genomic ranges (GTF, BED, VCF)

  Java

  •

  GNU General Public License v3.0

  •00 forks•00 stars•22 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• asap_web

  Public
  ASAP container for hosting the web portal

  JavaScript

  •

  GNU General Public License v3.0

  •00 forks•11 star•00 issues•00 pull requests•Updated Apr 8, 2026Apr 8, 2026

• asap_run

  Public
  ASAP container for running all pipeline code

  Java

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 1, 2026Apr 1, 2026

• scfair

  Public
  an initiative to standardize single-cell genomics data and promote findable, accessible, interoperable, and reusable single-cell data.

  Ruby

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 29, 2026Mar 29, 2026

• TFseqTools

  Public
  A suite of tools for the pre-processing of TF-seq data

  Java

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 20, 2026Mar 20, 2026

• meSMiLEseq

  Public
  Material and source code for meSMiLEseq paper

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 18, 2026Mar 18, 2026

• Neuro_Droso_ND75KD

  Public
  ND75KD project

  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 11, 2026Mar 11, 2026

• ASAP

  Public
  ASAP : Automated Single-cell Analysis Pipeline

  visualizationbioinformaticsenrichment+ 17

  visualizationbioinformaticsenrichmentrna-seqclusteringweb-appgene-expressionontologyweb-applicationbioinformatics-pipeline+ 10

  GNU General Public License v3.0

  •1010 forks•2727 stars•1010 issues•00 pull requests•Updated Mar 10, 2026Mar 10, 2026

• ECCB-2026

  Public
  SIB Community Days - Single-cell and spatial data FAIRification, community standards and training

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 9, 2026Mar 9, 2026

• ChromatinHD

  Public
  High-definition modeling of chromatin + transcriptomics data

  Python

  •

  MIT License

  •00 forks•2626 stars•1010 issues•00 pull requests•Updated Jan 27, 2026Jan 27, 2026

• scCM

  Public
  Benchmarking framework for chromatin module detection across bulk and single-cell modalities (semester project, Deplancke Lab, EPFL)

  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 22, 2026Jan 22, 2026

• BRB-seqTools

  Public
  Suite of tools for processing BRB-seq data

  Java

  •

  Other

  •1010 forks•3030 stars•00 issues•00 pull requests•Updated Jan 19, 2026Jan 19, 2026

• TF-seq

  Public
  Material and source code for TF-seq manuscript

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •00 forks•33 stars•11 issue•00 pull requests•Updated Jan 13, 2026Jan 13, 2026

• IRIS

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 16, 2025Dec 16, 2025

• dgrpool_web

  Public
  DGRPool is a web application designed to serve as a comprehensive repository for Drosophila Genetic Reference Panel (DGRP) phenotyping datasets.

  Ruby

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 9, 2025Oct 9, 2025

• scfair-manuscript

  Public
  Material and source code for the scFAIR manuscript

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 25, 2025Sep 25, 2025

• asap_old

  Public
  ASAP container for running old website (v1)

  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 14, 2025May 14, 2025

• dgrpool

  Public
  Scripts used for the DGRPool ELife manuscript

  R

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 5, 2025May 5, 2025

• CAS-scRNAseq-2025

  Public
  CAS-PMO_Ed.5-M3: Single-cell RNA-seq analysis (Lecture + Hands-on)

  data-sciencedatabioinformatics+ 2

  data-sciencedatabioinformaticssingle-cellsingle-cell-rna-seq

  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 11, 2025Apr 11, 2025

• EXTRA-seq

  Public
  Scripts for the EXTRA-seq manuscript

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Feb 15, 2025Feb 15, 2025

• Context-TFs

  Public
  Material and source code for Kribelbauer et al.

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •11 fork•00 stars•00 issues•00 pull requests•Updated Feb 3, 2025Feb 3, 2025

• ChromatinHD_manuscript

  Public
  Python

  •00 forks•11 star•00 issues•00 pull requests•Updated Dec 13, 2024Dec 13, 2024

• SIB-ASAP-2024

  Public
  Using ASAP for Single-Cell Analysis - 2024 Course

  GNU General Public License v3.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 5, 2024Nov 5, 2024

• Chromatin_modules

  Public
  Chromatin Modules across cell types.The code

  Jupyter Notebook

  •

  MIT License

  •00 forks•44 stars•00 issues•00 pull requests•Updated Oct 25, 2024Oct 25, 2024

• updeplasrv1

  Public
  Scripts for updeplasrv1 Web server (Dockerized)

  CSS

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 5, 2024Apr 5, 2024

• Numts_Aaeg

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 12, 2023Dec 12, 2023

• SIB-ASAP-2023

  Public
  Using ASAP for Single-Cell Analysis - 2023 Course

  Creative Commons Zero v1.0 Universal

  •11 fork•22 stars•00 issues•00 pull requests•Updated Nov 21, 2023Nov 21, 2023

• Meireles-Filho_Litovchenko2019

  Public
  Source code to support the paper: “Extensive tissue-specific expression variation and novel regulators underlying circadian behavior”

  bashrrna-seq-analysis+ 3

  bashrrna-seq-analysisngs-analysisdgrpcircadian-rhythms

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 16, 2023Jan 16, 2023

• BIO373_GeneticsAndGenomics

  Public
  Biofinformatics support for the Genetics and Genomics class (BIO373)

  HTML

  •

  GNU General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Nov 11, 2022Nov 11, 2022

• ENHPATHY4

  Public
  ENHPATHY Event IV - Hands-on session on analyzing single-cell data

  visualizationanalysistranscriptomics+ 1

  visualizationanalysistranscriptomicssingle-cell

  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Nov 10, 2022Nov 10, 2022