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.

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

For the workflow, see the motif_database_comparison.

For the workflow see de_novo_benchmark.

The analysis is detailed in this notebook.

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