Repositories list

• derfinderPlot

  Public
  Plotting functions for derfinder results

  rrstatsbioconductor+ 2

  rrstatsbioconductorrnaseqderfinder

  R

  •0•2•0•0•Updated Sep 26, 2025Sep 26, 2025

• regionReport

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

  rrmarkdownrstats+ 6

  rrmarkdownrstatsbioconductorrnaseqdeseq2derfinderedgerregionreport

  R

  •4•10•1•0•Updated Jan 14, 2025Jan 14, 2025

• recount-website

  Public
  Code for the Recount project

  rrstatsbioconductor+ 3

  rrstatsbioconductorrnaseqannotation-agnosticrecount

  R

  •

  MIT License

  •5•11•0•0•Updated Dec 13, 2024Dec 13, 2024

• recount

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

  countgener+ 11

  countgenerhumanrstatsbioconductorrnaseqdeseq2illuminaexon+ 4

  R

  •9•41•1•0•Updated Dec 12, 2024Dec 12, 2024

• derfinderData

  Public
  Example data used by the derfinder and derfinderData Bioconductor packages

  rrstatsbioconductor+ 2

  rrstatsbioconductorrnaseqderfinder

  R

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• derfinderHelper

  Public
  Helper package for derfinder

  rrstatsbioconductor+ 1

  rrstatsbioconductorderfinder

  R

  •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

• enrichedRanges

  Public
  enrichedRanges

  R

  •1•2•0•0•Updated May 7, 2023May 7, 2023

• postpi

  Public
  R

  •4•23•0•1•Updated Oct 29, 2021Oct 29, 2021

• swfdr

  Public
  Science-wise false discovery rate package

  R

  •3•3•2•0•Updated Dec 10, 2020Dec 10, 2020

• derCountSupp

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated Aug 23, 2019Aug 23, 2019

• libd_n36

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

  Shell

  •

  MIT License

  •1•1•0•0•Updated Aug 23, 2019Aug 23, 2019

• derSoftware

  Public
  Analyses for derfinder software paper

  HTML

  •

  MIT License

  •0•0•0•0•Updated Aug 23, 2019Aug 23, 2019

• derSupplement

  Public
  rrmarkdownrstats+ 3

  rrmarkdownrstatsbioconductorrnaseqderfinder

  HTML

  •

  MIT License

  •1•0•0•0•Updated Aug 23, 2019Aug 23, 2019

• recount-analyses

  Public
  Example analyses using recount

  rrmarkdownrstats+ 4

  rrmarkdownrstatsbioconductorrnaseqannotation-agnosticrecount

  HTML

  •

  Creative Commons Attribution 4.0 International

  •0•2•0•0•Updated Aug 23, 2019Aug 23, 2019

• regionReportSupp

  Public
  Supplementary material for regionReport paper

  rrmarkdownrstats+ 3

  rrmarkdownrstatsbioconductorrnaseqregionreport

  HTML

  •

  MIT License

  •0•1•0•0•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

  •3•16•0•0•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

  •9•8•2•1•Updated Mar 25, 2019Mar 25, 2019

• recount-contributions

  Public
  Contribute your human Illumina RNA-seq data to recount2

  rrstatsbioconductor+ 3

  rrstatsbioconductorrnaseqannotation-agnosticrecount

  MIT License

  •3•5•0•0•Updated Jul 24, 2018Jul 24, 2018

• explanatory_language

  Public
  Data and code for the explanatory language paper

  HTML

  •2•2•0•1•Updated Jun 26, 2018Jun 26, 2018

• phenopredict

  Public
  Use gene expression to predict phenotype sample information

  R

  •5•19•2•0•Updated Feb 13, 2018Feb 13, 2018

• genesigprecision

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

  R

  •0•0•0•0•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

  •0•2•6•0•Updated Nov 20, 2015Nov 20, 2015

• tablemaker

  Public
  Preprocessing software for prepping Cufflinks output for Ballgown

  C++

  •5•6•1•0•Updated Nov 12, 2015Nov 12, 2015

• SRAmetadata

  Public
  HTML

  •0•6•3•0•Updated Oct 18, 2015Oct 18, 2015

• testCNAME

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

  HTML

  •1•0•0•0•Updated Jun 23, 2015Jun 23, 2015

• Set

  Public
  Set package

  R

  •2•3•0•0•Updated Apr 28, 2015Apr 28, 2015

• derTutor

  Public
  HTML

  •0•0•0•0•Updated Apr 10, 2015Apr 10, 2015

• polyester_code

  Public
  code used for analysis presented in polyester paper

  HTML

  •3•8•0•0•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

  •10•22•4•1•Updated Mar 6, 2015Mar 6, 2015

• testsetbias

  Public
  Materials to reproduce test set bias analysis.

  R

  •3•2•0•0•Updated Feb 13, 2015Feb 13, 2015