seeker

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.

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