Simplified Fetching and Processing of Microarray and RNA-Seq Data

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Documentation for package ‘seeker’ version 1.1.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

checkDefaultCommands	Check for presence of command-line interfaces
fastqc	Run FastQC
fastqscreen	Run FastQ Screen
fetch	Fetch files
fetchMetadata	Fetch metadata for a genomic study
getPlatforms	Get supported microarray platforms
getSalmonMetadata	Aggregrate metadata from salmon quantifications
getTx2gene	Get mapping between transcripts and genes
installCustomCdfPackages	Install custom CDF packages
installSysDeps	Install seeker's system dependencies
multiqc	Run MultiQC
salmon	Run Salmon
seeker	Process RNA-seq data end to end
seekerArray	Process microarray data end to end
trimgalore	Run Trim Galore!
tximport	Run tximport on RNA-seq quantifications