Status: Travis CI , Codecov

recount.bwtool

Compute coverage matrices from recount using bwtool. This makes it easy to explore regions beyond the genes and exons that are available in recount. For example, it can be used for annotation-agnostic differential expression analyses with the data from the recount project as described in the paper. This package was used for computing expressed regions in the GTEx data as described in this pre-print.

For more information about recount.bwtool check the help page for the coverage_matrix_bwtool() function.

Installation instructions

Get R 3.5.x from CRAN. Also install bwtool. Check it's installation instructions.

## Install the dependencies from Bioconductor
install.packages("BiocManager")
BiocManager::install(c('recount'))

## Then install recount.bwtool
BiocManager::install('LieberInstitute/recount.bwtool')

Install bwtool on SciServer

Thanks to @BenLangmead, you can install bwtool on SciServer Compute with these commands:

conda config --add channels conda-forge
conda config --add channels defaults
conda config --add channels r
conda config --add channels bioconda

conda install libpng

export CPATH="$CPATH:$HOME/miniconda3/include"
export LIBRARY_PATH="$LIBRARY_PATH:$HOME/miniconda3/lib"
export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/miniconda3/lib"

git clone https://github.com/CRG-Barcelona/libbeato.git
git clone https://github.com/CRG-Barcelona/bwtool.git
cd libbeato/
./configure --prefix=$HOME CFLAGS="-g -O0 -I${HOME}/include" LDFLAGS=-L${HOME}/lib
make
make install
cd ../bwtool/
./configure --prefix=$HOME CFLAGS="-g -O0 -I${HOME}/include" LDFLAGS=-L${HOME}/lib
make
make install

which would make bwtool available at /home/idies/bin/bwtool.

Citation

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

To cite the recount.bwtool package in publications use:

Ellis SE, Collado-Torres L, Jaffe AE, Leek JT (2018). “Improving the value of public RNA-seq expression data by phenotype prediction.” Nucl. Acids Res.. doi: 10.1093/nar/gky102 (URL: http://doi.org/10.1093/nar/gky102), <URL: https://doi.org/10.1093/nar/gky102>.

A BibTeX entry for LaTeX users is

@Article{,
    title = {Improving the value of public RNA-seq expression data by phenotype prediction},
    author = {Shannon E. Ellis and Leonardo Collado-Torres and Andrew E. Jaffe and Jeffrey T. Leek},
    year = {2018},
    journal = {Nucl. Acids Res.},
    doi = {10.1093/nar/gky102},
    url = {https://doi.org/10.1093/nar/gky102},
}

To cite recount use citation('recount') in R and 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>.

@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 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.