seeker is an R package for fetching and processing sequencing data, especially RNA-seq data, as well as microarray data. Hopefully it helps you get what you’re after, before the day you die. For more details, see Schoenbachler and Hughey (2022).
seeker, you can install
seeker and its dependencies, or use a pre-built Docker image in which
seeker and its dependencies are already installed.
seekerR package, either from CRAN or from the Hughey Lab drat repository. We use
BiocManager::install()in order to smoothly install
seeker’s dependencies that are on Bioconductor.
BiocManager::install('seeker') # CRAN # BiocManager::install('seeker', site_repository = 'https://hugheylab.github.io/drat/') # drat
Install the system dependencies to fetch and process sequencing data. The simplest way to do this is to use the function
installSysDeps(). For example,
seeker::installSysDeps('~', '~', '~', '~')
You can also use
installSysDeps()to fetch genomes from refgenie, such as those required to quantify transcript abundances using salmon.