Package: seeker
Type: Package
Title: Simplified Fetching and Processing of Microarray and RNA-Seq
        Data
Version: 1.0.10
Authors@R: c(
  person('Jake', 'Hughey', , 'jakejhughey@gmail.com', role = c('aut', 'cre')),
  person('Josh', 'Schoenbachler', , 'josh.schoenbachler@gmail.com', role = 'aut'))
Description: 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>.
URL: https://seeker.hugheylab.org, https://github.com/hugheylab/seeker
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.2.1
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)
Config/testthat/edition: 3
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2022-09-19 17:34:42 UTC; jakehughey
Author: Jake Hughey [aut, cre],
  Josh Schoenbachler [aut]
Maintainer: Jake Hughey <jakejhughey@gmail.com>
Repository: CRAN
Date/Publication: 2022-09-19 23:06:07 UTC
