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

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 t

SUBMITTER: Schoenbachler JL 

PROVIDER: S-EPMC9648347 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature