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README.md

Status: Travis CI Build Status, Bioc-release , Bioc-devel .

Bioc-release , Bioc-devel , Codecov codecov.io

recount

Explore and download data from the recount project available at the recount2 website. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project.

For more information about recount check the vignettes.

Installation instructions

Get R 3.3.x from CRAN.

## From Bioconductor
source('http://bioconductor.org/biocLite.R')
biocLite('recount')

## Suggested:
biocLite(c('derfinder', 'DESeq2'))

Vignettes

The vignettes for this package can be viewed via Bioconductor's website.

Citation

Below is the citation output from using citation('recount') in R. Please run this yourself to check for any updates on how to cite recount.

To cite the recount package in publications use:

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B and Leek JT (2017). “Reproducible RNA-seq analysis using recount2.” Nature Biotechnology. doi: 10.1038/nbt.3838 (URL: http://doi.org/10.1038/nbt.3838), <URL: http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html>.

A BibTeX entry for LaTeX users is

@Article{, title = {Reproducible RNA-seq analysis using recount2}, author = {Leonardo Collado-Torres and Abhinav Nellore and Kai Kammers and Shannon E. Ellis and Margaret A. Taub and Kasper D. Hansen and and Andrew E. Jaffe and Ben Langmead and Jeffrey T. Leek}, year = {2017}, journal = {Nature Biotechnology}, doi = {10.1038/nbt.3838}, url = {http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html}, }

Testing

Testing on Bioc-devel is feasible thanks to R Travis as well as Bioconductor's nightly build.