homer

HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.

The HOMER MultiQC module currently only parses output from the findPeaks tool. If you would like support to be added for other HOMER tools, please open a new issue on the MultiQC GitHub page.

FindPeaks

The HOMER findPeaks MultiQC module parses the summary statistics found at the top of HOMER peak files. Three key statistics are shown in the General Statistics table, all others are saved to multiqc_data/multiqc_homer_findpeaks.txt.

TagDirectory

The HOMER tag directory submodule parses output from files tag directory output files, generating a number of diagnostic plots.