Function reference • seeker

All functions

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