Simplified Fetching and Processing of Microarray and RNA-Seq
Data
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) ,
'ArrayExpress' Kauffmann et al. (2009) ,
Robust multi-array average 'RMA' Irizarry et al. (2003) ,
and 'BrainArray' Dai et al. (2005) .
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 ,
performs quality control checks using 'FastQC' Andrews ,
quantifies transcript abundances using 'salmon' Patro et al. (2017) and potentially
'refgenie' Stolarczyk et al. (2020) ,
aggregates the results using 'MultiQC' Ewels et al. (2016) ,
maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) ,
and summarizes transcript-level quantifications for gene-level analyses using
'tximport' Soneson et al. (2015) .