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.

Installation

Docker image

seeker and its dependencies are available in a Docker image called socker, based on rocker/rstudio.

docker pull ghcr.io/hugheylab/socker

If you don’t want to use Docker, you can follow the instructions below.

R package

1. Install BiocManager.

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

2. If you use RStudio, go to Tools → Global Options… → Packages → Add… (under Secondary repositories), then enter:

   • Name: hugheylab
   • Url: https://hugheylab.github.io/drat/

   You only have to do this once. Then you can install or update the package by entering:

   BiocManager::install('seeker')

   Alternatively, you can install or update the package by entering:

   BiocManager::install('seeker', site_repository = 'https://hugheylab.github.io/drat/')

System dependencies

If not using the docker image, use seeker::installSysDeps() to conveniently install and configure the various programs required to fetch and process sequencing data.

Usage

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