Three examples of using GimmeMotifs

This repository contains the analysis code of the manuscript describing the 2018 release of GimmeMotifs, an analysis framework for transcription factor motif analysis. The manuscript is available on biorRxiv as a preprint and can be cited as:

GimmeMotifs: an analysis framework for transcription factor motif analysis
Niklas Bruse, Simon J. van Heeringen
bioRxiv (2018) DOI: 10.1101/474403

The manuscript source can be found at https://github.com/simonvh/gimmemotifs-manuscript.

Motif database benchmark

We evaluated nine different TF motif databases using ChIP-seq peaks from ReMap.

For the workflow, see the motif_database_comparison.

Benchmark of de novo motif finders

For the workflow see de_novo_benchmark.

Motif activity in hematopoietic enhancers

The analysis is detailed in this notebook.

GimmeMotifs vertebrate v5.0

The pipeline that was used to create the clustered, non-redundant motif database GimmeMotifs vertebrate v5.0 can be found here: cluster_motifs.