GimmeMotifs for transcription factor motif analysis¶
What is GimmeMotifs?¶
GimmeMotifs is an analysis framework for transcription factor motif analysis written in Python. It contains command-line scripts to predict de novo motifs, scan for known motifs, identify differential motifs, calculate motif enrichment statistics, plot sequence logos and more. In addition, all this functionality is available from a Python API.
GimmeMotifs is free and open source research software. If you find it useful please cite our paper:
Bruse N and van Heeringen SJ, GimmeMotifs: an analysis framework for transcription factor motif analysis, bioRxiv, 2018. https://www.biorxiv.org/content/10.1101/474403v1.full. doi: 10.1101/474403.
van Heeringen SJ and Veenstra GJC, GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments, Bioinformatics. 2011 Jan 15;27(2):270-1. doi: 10.1093/bioinformatics/btq636.
Have a look at these simple examples to get a taste of what is possible.
Check out the more detailed tutorials.
Full command-line reference can be found here.
There’s also an API documentation.
- Simple examples
- Command-line reference
- API documentation
- SQLite error when running on a cluster
- ImportError: dlopen: cannot load any more object with static TLS
- ‘i’ format requires -2147483648 <= number <= -2147483646
- Sorry, motif prediction tool [X] is not supported
- I get motifs that have differential scores in gimme maelstrom, however, the number is not different across clusters
- I have upgraded GimmeMotifs and now it doesn’t find my genome
- I cannot run gimme index anymore
- I get ‘RuntimeError: Invalid DISPLAY variable’
- I get a KeyError when running gimme maelstrom