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.
Install the package (see below) and run the following:
help(package=smallCAGEqc)
devtools::install_github('charles-plessy/smallCAGEqc', upgrade_dependencies = FALSE)
You may need to enable the Bioconductor repository by running setRepositories() first.
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)'