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bioRxiv · 10.1101/2022.08.30.505820

The seeker R package: simplified fetching and processing of transcriptome data

Schoenbachler, J. L.·Hughey, J. J.
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Abstract

Transcriptome data have become invaluable for interrogating biological systems. Preparing a transcriptome dataset for analysis, particularly an RNA-seq dataset, entails multiple steps and software programs, each with its own command-line interface (CLI). Although these CLIs are powerful, they often require shell scripting for automation and parallelization, which can have a high learning curve, especially when the details of the CLIs vary from one tool to another. However, many individuals working with transcriptome data are already familiar with R due to the plethora and popularity of R-based tools for analyzing biological data. Thus, we developed an R package called seeker for simplified fetching and processing of RNA-seq and microarray data. Seeker is a wrapper around various existing tools, and provides a standard interface, simple parallelization, and detailed logging. Seekers primary output--sample metadata and gene expression values based on Entrez or Ensembl Gene IDs--can be directly plugged into a differential expression analysis. To maximize reproducibility, seeker is available as a standalone R package and in a Docker image that includes all dependencies, both of which are accessible at https://seeker.hugheylab.org.

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Schoenbachler, J. L., Hughey, J. J.. 2022-09-01. The seeker R package: simplified fetching and processing of transcriptome data. https://doi.org/10.1101/2022.08.30.505820

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