GimmeMotifs
Gimmemotifs is a suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See the documentation for detailed installation instructions and usage examples.
Easy installation
The most straightforward way to install GimmeMotifs is via conda using the bioconda channel.
If you have not used bioconda before, first set up the necessary channels (in this order!). You only have to do this once.
$ conda config --add channels bioconda
$ conda config --add channels conda-forge
You can now install GimmeMotifs with one command:
# Create an environment called gimme with all dependencies
$ conda create -n gimme gimmemotifs-minimal
# or
$ conda create -n gimme gimmemotifs
# Activate the environment
$ conda activate gimme
Don't forget to activate the environment with conda activate gimme whenever you want to use GimmeMotifs.
Quick start
Predict some de novo motifs:
$ gimme motifs my_peaks.bed my_motifs -g /data/genomes/hg38/hg38.fa --denovo
Download a genome
The example above assumes that you have the hg38 genome in /data/genomes/hg38/hg38.fa.
GimmeMotifs can also use genomes installed by genomepy.
You can configure the directory where genomepy stores genomes by editing
~/.config/genomepy/genomepy.yaml
genome_dir: /data/genomes
To download a genome from UCSC:
$ genomepy install hg38 --annotation
Now you can specify this genome for GimmeMotifs by name.
$ gimme motifs my_peaks.bed -g hg38 -n my_motifs
Cite us
The manuscript describing this latest release 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
We need your help!
GimmeMotifs was originally developed for our own needs but we would really like it to be useful to the wider community. However, this also depends on your input. Let us know what you think! What features are missing? Which tutorial would you like to see? What part of the documentation is unclear? Have great ideas for future developments? Maybe you even want to join in developing this software?
Help
- Full documentation: http://gimmemotifs.readthedocs.io/
- Check the FAQ for common issues
- The preferred way to get support is through the GitHub issues page
- Finally, you can reach me by mail
Release files for gimmemotifs 0.18.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | |
|---|---|---|---|---|
| gimmemotifs-0.18.4.tar.gz | 12.2 MB | Without provenance | Details |
Release files / gimmemotifs-0.18.4.tar.gz
| Download URL | gimmemotifs-0.18.4.tar.gz |
|---|---|
| Size | 12.2 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
6da4020f774ebbaa28d4ca4f21b0fe7bad8f2e3c5fe8239ccd2557361174aba7
|
|
BLAKE2b-256 checksum How to use checksums |
6622829aacbb78293d55e3a67934f9393b14c981a353967aa2b60a02b3320f43
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/6.2.0 CPython/3.12.13
|
Security for gimmemotifs 0.18.4
Provenance
Provenance describes where a file came from. On PyPI, provenance is shared via attestations, which provide a verifiable record of the build or publishing details. View details, limitations and caveats.
No provenance found
None of the files in this release were uploaded with provenance metadata.
A note on package security
PyPI is a repository for distributing packages, not a service for auditing them. While third-party security researchers and our staff do their best to detect and remove malicious packages, PyPI cannot guarantee the quality, security or suitability of any given package.
To learn more about protecting yourself from malicious actors, visit our package security documentation.
