universalmotif

A Toolkit for Sequence Motif Analysis

Bioconductor version: 3.24 · Package version: 1.31.54

A comprehensive toolkit for working with sequence motifs in R. Imports and exports most common motif formats (JASPAR, MEME, HOMER, TRANSFAC, CIS-BP, UNIPROBE) and interoperates with the other Bioconductor motif packages. Analysis functions cover de novo motif discovery, motif-vs-motif comparison and clustering, P-value calculation, sequence scanning, enrichment against shuffled or composition-matched backgrounds, positional bias testing, and pairwise motif co-occurrence. Also includes utilities for sequence shuffling, motif trimming, higher-order representations, ground-truth simulation by motif implantation, and logo-plotting functionality.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("universalmotif")