seeker

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).

Installation

To use seeker, you can install seeker and its dependencies, or use a pre-built Docker image in which seeker and its dependencies are already installed.

R package and dependencies

1. Install the BiocManager R package.

   if (!requireNamespace('BiocManager', quietly = TRUE))
     install.packages('BiocManager')

2. Install the seeker R 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

3. 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.

Docker image

The Docker image is called socker and is based on rocker/rstudio.

docker pull ghcr.io/hugheylab/socker

Usage

For an introduction to the package, read the vignette. For more details, check out the reference documentation.