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.