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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 |
Please use the canonical form https://CRAN.R-project.org/package=seeker to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.