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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "seeker" in publications use:'
type: software
license: MIT
title: 'seeker: Simplified Fetching and Processing of Microarray and RNA-Seq Data'
version: 1.1.6
doi: 10.32614/CRAN.package.seeker
abstract: 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) <https://doi.org/10.1093/bioinformatics/btm254>, 'ArrayExpress' Kauffmann
  et al. (2009) <https://doi.org/10.1093/bioinformatics/btp354>, Robust multi-array
  average 'RMA' Irizarry et al. (2003) <https://doi.org/10.1093/biostatistics/4.2.249>,
  and 'BrainArray' Dai et al. (2005) <https://doi.org/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) <https://doi.org/10.1038/nmeth.4197>
  and potentially 'refgenie' Stolarczyk et al. (2020) <https://doi.org/10.1093/gigascience/giz149>,
  aggregates the results using 'MultiQC' Ewels et al. (2016) <https://doi.org/10.1093/bioinformatics/btw354>,
  maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) <https://doi.org/10.1038/nprot.2009.97>,
  and summarizes transcript-level quantifications for gene-level analyses using 'tximport'
  Soneson et al. (2015) <https://doi.org/10.12688/f1000research.7563.2>.
authors:
- family-names: Hughey
  given-names: Jake
  email: jakejhughey@gmail.com
- family-names: Schoenbachler
  given-names: Josh
  email: josh.schoenbachler@gmail.com
repository: https://cranhaven.r-universe.dev
repository-code: https://github.com/hugheylab/seeker
commit: 911db8ed9448b270f67ce78dcb8128ebec4411b2
url: https://seeker.hugheylab.org
date-released: '2024-08-27'
contact:
- family-names: Hughey
  given-names: Jake
  email: jakejhughey@gmail.com