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: | 1.1.6 |
| Depends: | R (≥ 3.5) |
| Imports: | affy (≥ 1.68.0), AnnotationDbi (≥ 1.52.0), BiocManager (≥ 1.30.0), biomaRt (≥ 2.36.1), checkmate (≥ 2.1.0), 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: | ArrayExpress (≥ 1.62.0), Biobase, doParallel (≥ 1.0.17), knitr, org.Mm.eg.db, rmarkdown, testthat (≥ 3.1.0) |
| Published: | 2024-08-27 |
| DOI: | 10.32614/CRAN.package.seeker |
| 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 |
| In views: | Omics |
| CRAN checks: | seeker results |
| Reference manual: | seeker.pdf |
| Vignettes: |
Introduction to seeker (source, R code) Reproducibility with seeker (source, R code) |
| Package source: | seeker_1.1.6.tar.gz |
| Windows binaries: | r-devel: seeker_1.1.6.zip, r-release: seeker_1.1.6.zip, r-oldrel: seeker_1.1.6.zip |
| macOS binaries: | r-release (arm64): seeker_1.1.6.tgz, r-oldrel (arm64): seeker_1.1.6.tgz, r-release (x86_64): seeker_1.1.6.tgz, r-oldrel (x86_64): seeker_1.1.6.tgz |
| Old sources: | seeker archive |
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