leekgroup/testsetbias

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Created over 10 years ago
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leekgroup/testsetbias

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Materials to reproduce test set bias analysis.

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"

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

SRAmetadata

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.

recount-contributions

Contribute your human Illumina RNA-seq data to recount2

tablemaker

Preprocessing software for prepping Cufflinks output for Ballgown

swfdr

Science-wise false discovery rate package

derfinderPlot

Plotting functions for derfinder results

Set

enrichedRanges

sig2trial

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

recount-analyses

Example analyses using recount

explanatory_language

Data and code for the explanatory language paper

regionReportSupp

Supplementary material for regionReport paper

libd_n36

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