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README.md

smallCAGEqc

smallCAGEqc is a R package collecting scripts for the analysis of transcriptome libraries at RIKEN CLST/DGT ex-OSC. It makes strong assumptions on our infrastructure and hardcodes paths for key files, therefore, although it shared on GitHub, there is really no guaranty that it will be useful to you if we are not working together already. It installs a Rmarkdown template for analyses on Rstudio.

Need help ?

Install the package (see below) and run the following:

help(package=smallCAGEqc)

Installation on Linux computers

From GitHub in R (recommended)

devtools::install_github('charles-plessy/smallCAGEqc', upgrade_dependencies = FALSE)

You may need to enable the Bioconductor repository by running setRepositories() first.

From a Git clone.

git clone https://github.com/charles-plessy/smallCAGEqc.git
R CMD INSTALL smallCAGEqc

In case of error no permission to install to directory ‘/usr/local/lib/R/site-library’, create a local R directory with the following command.

/usr/bin/Rscript -e 'dir.create(Sys.getenv("R_LIBS_USER"), recursive=TRUE)'
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