seeker: Simplified Fetching and Processing of Microarray and RNA-Seq Data

Wrapper around various existing tools and command-line interfaces, providing a standard interface, simple parallelization, and detailed logging. For microarray data, maps probe sets to standard gene IDs, building on 'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>, 'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>, Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>, and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>. For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>, performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>, quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197> and potentially 'refgenie' Stolarczyk et al. (2020) <doi:10.1093/gigascience/giz149>, aggregates the results using 'MultiQC' Ewels et al. (2016) <doi:10.1093/bioinformatics/btw354>, maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) <doi:10.1038/nprot.2009.97>, and summarizes transcript-level quantifications for gene-level analyses using 'tximport' Soneson et al. (2015) <doi:10.12688/f1000research.7563.2>.

Version: 1.0.10
Depends: R (≥ 3.5)
Imports: affy (≥ 1.68.0), AnnotationDbi (≥ 1.52.0), ArrayExpress (≥ 1.50.0), BiocManager (≥ 1.30.0), biomaRt (≥ 2.36.1), checkmate (≥ 2.0.0), curl (≥ 3.2), data.table (≥ 1.11.8), foreach (≥ 1.4.4), GEOquery (≥ 2.58.0), glue (≥ 1.5.0), jsonlite (≥ 1.7.2), methods, qs (≥ 0.21.2), R.utils (≥ 2.11.0), RCurl (≥ 1.98), readr (≥ 1.4.0), sessioninfo (≥ 1.2.0), tximport (≥ 1.8.0), withr (≥ 2.4.2), yaml (≥ 2.2.1)
Suggests: Biobase, doParallel (≥ 1.0.16), knitr, org.Mm.eg.db, rmarkdown, testthat (≥ 3.1.0)
Published: 2022-09-19
Author: Jake Hughey [aut, cre], Josh Schoenbachler [aut]
Maintainer: Jake Hughey <jakejhughey at gmail.com>
License: MIT + file LICENSE
URL: https://seeker.hugheylab.org, https://github.com/hugheylab/seeker
NeedsCompilation: no
CRAN checks: seeker results

Documentation:

Reference manual: seeker.pdf
Vignettes: Introduction to seeker
Reproducibility with seeker

Downloads:

Package source: seeker_1.0.10.tar.gz
Windows binaries: r-devel: seeker_1.0.10.zip, r-release: seeker_1.0.10.zip, r-oldrel: seeker_1.0.10.zip
macOS binaries: r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available
Old sources: seeker archive

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