installCustomCdfPackages

Install Brainarray custom CDFs for processing raw Affymetrix data. See
<a href="http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp">http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp</a>.

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

installCustomCdfPackages function

<dl><dt>pkgs</dt>
<dd>Character vector of package names, e.g., "hgu133ahsentrezgcdf".</dd>
<dt>ver</dt>
<dd>Integer version number (25 as of 5 Jan 2021).</dd>
<dt>dryRun</dt>
<dd>Logical indicating whether to actually install the packages.</dd></dl>

Arguments

Install Brainarray custom CDFs for processing raw Affymetrix data. See
<a href='http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp'>http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp</a>.

Install custom CDF packages — installCustomCdfPackages

<dl>

<dt>pkgs</dt>
<dd>Character vector of package names, e.g., "hgu133ahsentrezgcdf".</dd>


<dt>ver</dt>
<dd>Integer version number (25 as of 5 Jan 2021).</dd>


<dt>dryRun</dt>
<dd>Logical indicating whether to actually install the packages.</dd>

</dl>

installCustomCdfPackages: Install custom CDF packages

Description

Usage

Value

Arguments