Repositories list

• recount

  Public
  R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

  countgener+ 11

  countgenerhumanrstatsbioconductorrnaseqdeseq2illuminaexon+ 4

  R

  •99 forks•4141 stars•11 issue•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• regionReport

  Public
  Generate HTML report for a set of genomic regions or DESeq2/edgeR results

  rrmarkdownrstats+ 6

  rrmarkdownrstatsbioconductorrnaseqdeseq2derfinderedgerregionreport

  R

  •44 forks•99 stars•11 issue•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• derfinderPlot

  Public
  Plotting functions for derfinder results

  rrstatsbioconductor+ 2

  rrstatsbioconductorrnaseqderfinder

  R

  •00 forks•22 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• derfinderHelper

  Public
  Helper package for derfinder

  rrstatsbioconductor+ 1

  rrstatsbioconductorderfinder

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• derfinderData

  Public
  Example data used by the derfinder and derfinderData Bioconductor packages

  rrstatsbioconductor+ 2

  rrstatsbioconductorrnaseqderfinder

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

• recount-website

  Public
  Code for the Recount project

  rrstatsbioconductor+ 3

  rrstatsbioconductorrnaseqannotation-agnosticrecount

  R

  •

  MIT License

  •55 forks•1111 stars•00 issues•00 pull requests•Updated Dec 13, 2024Dec 13, 2024

• enrichedRanges

  Public
  enrichedRanges

  R

  •11 fork•22 stars•00 issues•00 pull requests•Updated May 7, 2023May 7, 2023

• postpi

  Public
  R

  •44 forks•2323 stars•00 issues•11 pull request•Updated Oct 29, 2021Oct 29, 2021

• swfdr

  Public
  Science-wise false discovery rate package

  R

  •33 forks•33 stars•22 issues•00 pull requests•Updated Dec 10, 2020Dec 10, 2020

• derCountSupp

  Public
  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 23, 2019Aug 23, 2019

• libd_n36

  Public
  derfinder analysis of LIBD post-mortem brain data (36 samples)

  Shell

  •

  MIT License

  •11 fork•11 star•00 issues•00 pull requests•Updated Aug 23, 2019Aug 23, 2019

• derSoftware

  Public
  Analyses for derfinder software paper

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Aug 23, 2019Aug 23, 2019

• derSupplement

  Public
  rrmarkdownrstats+ 3

  rrmarkdownrstatsbioconductorrnaseqderfinder

  HTML

  •

  MIT License

  •11 fork•00 stars•00 issues•00 pull requests•Updated Aug 23, 2019Aug 23, 2019

• recount-analyses

  Public
  Example analyses using recount

  rrmarkdownrstats+ 4

  rrmarkdownrstatsbioconductorrnaseqannotation-agnosticrecount

  HTML

  •

  Creative Commons Attribution 4.0 International

  •00 forks•22 stars•00 issues•00 pull requests•Updated Aug 23, 2019Aug 23, 2019

• regionReportSupp

  Public
  Supplementary material for regionReport paper

  rrmarkdownrstats+ 3

  rrmarkdownrstatsbioconductorrnaseqregionreport

  HTML

  •

  MIT License

  •00 forks•11 star•00 issues•00 pull requests•Updated Aug 23, 2019Aug 23, 2019

• networks_correction

  Public
  Code to reproduce analysis in "Addressing confounding artifacts in reconstruction of gene co-expression networks"

  HTML

  •33 forks•1616 stars•00 issues•00 pull requests•Updated Apr 22, 2019Apr 22, 2019

• locfdr-python

  Public
  Python implementation of Efron, Turnbull, and Narasimhan's R function locfdr v1.1-7, which computes local false discovery rates. See http://cran.r-project.org/w…

  Python

  •

  GNU General Public License v2.0

  •99 forks•88 stars•22 issues•11 pull request•Updated Mar 25, 2019Mar 25, 2019

• recount-contributions

  Public
  Contribute your human Illumina RNA-seq data to recount2

  rrstatsbioconductor+ 3

  rrstatsbioconductorrnaseqannotation-agnosticrecount

  MIT License

  •33 forks•55 stars•00 issues•00 pull requests•Updated Jul 24, 2018Jul 24, 2018

• explanatory_language

  Public
  Data and code for the explanatory language paper

  HTML

  •22 forks•22 stars•00 issues•11 pull request•Updated Jun 26, 2018Jun 26, 2018

• phenopredict

  Public
  Use gene expression to predict phenotype sample information

  R

  •55 forks•1919 stars•22 issues•00 pull requests•Updated Feb 13, 2018Feb 13, 2018

• genesigprecision

  Public
  Code for reproducing analysis for "Measuring the contribution of genomic..."

  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 10, 2015Dec 10, 2015

• sig2trial

  Public
  Pipeline R package for creating simple gene signatures and testing their value in a clinical trial setting

  R

  •00 forks•22 stars•66 issues•00 pull requests•Updated Nov 20, 2015Nov 20, 2015

• tablemaker

  Public
  Preprocessing software for prepping Cufflinks output for Ballgown

  C++

  •55 forks•66 stars•11 issue•00 pull requests•Updated Nov 12, 2015Nov 12, 2015

• SRAmetadata

  Public
  HTML

  •00 forks•66 stars•33 issues•00 pull requests•Updated Oct 18, 2015Oct 18, 2015

• testCNAME

  Public
  Test that transferring a repo and adding a CNAME doesn't break URLs

  HTML

  •11 fork•00 stars•00 issues•00 pull requests•Updated Jun 23, 2015Jun 23, 2015

• Set

  Public
  Set package

  R

  •22 forks•33 stars•00 issues•00 pull requests•Updated Apr 28, 2015Apr 28, 2015

• derTutor

  Public
  HTML

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 10, 2015Apr 10, 2015

• polyester_code

  Public
  code used for analysis presented in polyester paper

  HTML

  •33 forks•88 stars•00 issues•00 pull requests•Updated Mar 9, 2015Mar 9, 2015

• derfinder

  Public
  R package for DER Finder, a method for differential expression analysis of RNA-seq data

  R

  •

  MIT License

  •1010 forks•2222 stars•44 issues•11 pull request•Updated Mar 6, 2015Mar 6, 2015

• testsetbias

  Public
  Materials to reproduce test set bias analysis.

  R

  •33 forks•22 stars•00 issues•00 pull requests•Updated Feb 13, 2015Feb 13, 2015