ReCount

A multi-experiment resource of analysis-ready RNA-seq gene count datasets

ReCount is an online resource consisting of RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, we combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available here. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

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Related Tools

Myrna: Cloud, differential gene expression

Related Publications

Frazee AC, Langmead B, Leek JT. ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics 12:449

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The files below are needed to run the make_esets.r script. Count tables available for download have column names that have been changed from Myrna's default output, but the script uses the original column names; those count tables are below. Two additional files are also required: wormlabels.csv, a file used to properly label the modENCODE worm samples, and countflytechreps.csv, a .csv version of the modENCODE fly manifest used in the script to determine the number of tecnhical replicates for each sample.

Count Tables with original column names:

Other Files

wormlabels.csv
countflytechreps.csv