MotifFinder: Find enriched motifs in a set of DNA sequences

By Simon Myers, Nicolas Altemose & Daniel Wells

This is an R package for finding enriched motifs in a set of DNA sequences using an iterative Gibbs sampler described in Altemose et al. eLife 2017.

Installation & Usage

# install.packages("remotes")
remotes::install_github("myersgroup/MotifFinder")

library(MotifFinder)

# simulate set of sequences enriched for a motif
set.seed(42)
simulated_sequences <- simulate_sequences(motif="ATgTT_GtCC")

# run MotifFinder
motif_found <- findamotif(simulated_sequences, len=7)

# visualise the motif found
ggseqlogo::ggseqlogo(get_PWM(motif_found))

For more detailed examples of how to use this package please see the vignette.

This code is ported from the original at https://github.com/altemose/PRDM9-map

If you use this program, please cite Altemose et al. eLife 2017.

This is free software shared in the hope it may be of use; no warranty is given or implied.