Repositories list

• TF-seq

  Public
  Material and source code for TF-seq manuscript

  Jupyter Notebook

  •

  Creative Commons Zero v1.0 Universal

  •0•0•1•0•Updated Aug 13, 2025Aug 13, 2025

• scfair

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

  Ruby

  •0•0•13•0•Updated Jul 31, 2025Jul 31, 2025

• asap_run

  Public
  ASAP container for running all pipeline code

  Java

  •

  GNU General Public License v3.0

  •0•0•2•0•Updated Jul 21, 2025Jul 21, 2025

• meSMiLEseq

  Public
  Material and source code for meSMiLEseq paper

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

• Neuro_Droso_ND75KD

  Public
  ND75KD project

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 19, 2025Jun 19, 2025

• BRB-seqTools

  Public
  Suite of tools for processing BRB-seq data

  Java

  •

  Other

  •9•28•3•0•Updated Jun 3, 2025Jun 3, 2025

• ASAP

  Public
  ASAP : Automated Single-cell Analysis Pipeline

  visualizationbioinformaticsenrichment+ 17rna-seqclusteringweb-appgene-expressionontologyweb-applicationbioinformatics-pipeline+ 10

  GNU General Public License v3.0

  •10•27•14•0•Updated May 20, 2025May 20, 2025

• asap_old

  Public
  ASAP container for running old website (v1)

  JavaScript

  •0•0•0•0•Updated May 14, 2025May 14, 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

  •0•0•0•0•Updated May 5, 2025May 5, 2025

• dgrpool

  Public
  Scripts used for the DGRPool ELife manuscript

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 5, 2025May 5, 2025

• asap_web

  Public
  ASAP container for hosting the web portal

  HTML

  •

  GNU General Public License v3.0

  •0•1•1•0•Updated Apr 16, 2025Apr 16, 2025

• ChromatinHD

  Public
  High-definition modeling of chromatin + transcriptomics data

  Python

  •

  MIT License

  •0•24•9•0•Updated Apr 15, 2025Apr 15, 2025

• CAS-scRNAseq-2025

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

  data-sciencedatabioinformatics+ 2single-cellsingle-cell-rna-seq

  HTML

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

• FastReadCounter

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

  Java

  •

  GNU General Public License v3.0

  •0•0•2•0•Updated Feb 21, 2025Feb 21, 2025

• EXTRA-seq

  Public
  Scripts for the EXTRA-seq manuscript

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •0•0•0•0•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

  •1•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• ChromatinHD_manuscript

  Public
  Python

  •0•1•0•0•Updated Dec 13, 2024Dec 13, 2024

• SIB-ASAP-2024

  Public
  Using ASAP for Single-Cell Analysis - 2024 Course

  GNU General Public License v3.0

  •1•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• Chromatin_modules

  Public
  Chromatin Modules across cell types.The code

  Jupyter Notebook

  •

  MIT License

  •0•4•0•0•Updated Oct 25, 2024Oct 25, 2024

• updeplasrv1

  Public
  Scripts for updeplasrv1 Web server (Dockerized)

  CSS

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 5, 2024Apr 5, 2024

• TFseqTools

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

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 14, 2023Dec 14, 2023

• Numts_Aaeg

  Public
  HTML

  •0•0•0•0•Updated Dec 12, 2023Dec 12, 2023

• SIB-ASAP-2023

  Public
  Using ASAP for Single-Cell Analysis - 2023 Course

  Creative Commons Zero v1.0 Universal

  •1•2•0•0•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+ 3ngs-analysisdgrpcircadian-rhythms

  R

  •0•0•0•0•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

  •0•0•0•0•Updated Nov 11, 2022Nov 11, 2022

• ENHPATHY4

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

  visualizationanalysistranscriptomics+ 1single-cell

  HTML

  •1•0•0•0•Updated Nov 10, 2022Nov 10, 2022

• BRB-seq

  Public
  Code and scripts for reproducing figures of BRB-seq paper

  R

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 5, 2022Oct 5, 2022

• BeversLitovchenko2018

  Public
  Source code to support the paper: "Extensive mitochondrial population structure and haplotype-specific variation in metabolic phenotypes in the Drosophila Genetic Reference Panel"

  javabashr+ 5variant-callingngs-analysismitochondriadgrpnumts

  R

  •0•3•0•0•Updated Sep 9, 2022Sep 9, 2022

• Live-seq

  Public
  Live-seq

  R

  •

  GNU General Public License v3.0

  •4•9•0•0•Updated Aug 18, 2022Aug 18, 2022

• BiSS

  Public
  Yeast one-hybrid screening for DNA-protein interactions

  PHP

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 28, 2022Jun 28, 2022