Discover leekgroup/sig2trial Open Source project

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R
Created over 9 years ago
Updated about 9 years ago

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

recount

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

derfinder

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

postpi

phenopredict

Use gene expression to predict phenotype sample information

networks_correction

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

HTML

recount-website

Code for the Recount project

regionReport

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

ballgown_code

analysis code used in Ballgown paper

polyester_code

code used for analysis presented in polyester paper

HTML

SRAmetadata

HTML

locfdr-python

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/web/packages/locfdr/ for more information.

Python

recount-contributions

Contribute your human Illumina RNA-seq data to recount2

tablemaker

Preprocessing software for prepping Cufflinks output for Ballgown

C++

swfdr

Science-wise false discovery rate package

derfinderPlot

Plotting functions for derfinder results

Set

Set package

enrichedRanges

recount-analyses

Example analyses using recount

HTML

explanatory_language

Data and code for the explanatory language paper

HTML

testsetbias

Materials to reproduce test set bias analysis.

regionReportSupp

Supplementary material for regionReport paper

HTML

libd_n36

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

Shell

leekgroup/sig2trial

leekgroup

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