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 |