checkDefaultCommands

This function checks whether the command-line tools used by seeker are
accessible in the expected places.

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>.

Jake Hughey

seeker

Simplified Fetching and Processing of Microarray and RNA-Seq
Data

Josh Schoenbachler

checkDefaultCommands function

<dl><dt>keepIdx</dt>
<dd>Logical indicating whether to keep the <code>idx</code> column of the
resulting data.table. For internal use only.</dd></dl>

Arguments

Check for presence of command-line interfaces — checkDefaultCommands

<dl>

<dt>keepIdx</dt>
<dd>Logical indicating whether to keep the <code>idx</code> column of the
resulting data.table. For internal use only.</dd>

</dl>

checkDefaultCommands: Check for presence of command-line interfaces

Description

Usage

Value

Arguments

See Also