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.
docker pull ghcr.io/hugheylab/socker
If you don’t want to use Docker, you can follow the instructions below.
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:
Alternatively, you can install or update the package by entering:
BiocManager::install('seeker', site_repository = 'https://hugheylab.github.io/drat/')
If not using the docker image, use
seeker::installSysDeps() to conveniently install and configure the various programs required to fetch and process sequencing data.