DESCRIPTION

Package: seeker
Type: Package
Title: Simplified Fetching and Processing of Microarray and RNA-Seq Data
Version: 1.1.6
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
LazyData: true
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
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)
Config/testthat/edition: 3
VignetteBuilder: knitr