CEASp3

CEASp3 is a Python 3 port of the Cis-regulatory Element Annotation System (CEAS), a toolkit for annotating ChIP–seq peaks and generating signal profiles around genomic features.

Reference

If you use CEASp3 please cite:

H. Gene Shin, et al. "CEAS: cis-regulatory element annotation system." Bioinformatics 25(19):2605–2606, 2009.

Installation

1. Install the dependency:

   pip install -r requirements.txt
   

2. Install CEASp3:

   pip install .
   

   The scripts listed in bin/ such as ceas, ceasBW, sitepro, etc. will be placed on your PATH.

Example usage

Annotate ChIP peaks

Annotate a BED file of ChIP regions using a local gene table and generate enrichment profiles:

ceas -b peaks.bed -g refGene.sqlite --name my_chip

Wig signal profiling

Generate average signal plots around gene bodies from a WIG track:

ceas -w treat.wig -g refGene.sqlite --name treat_profile --rel-dist 3000 --pf-res 50

BigWig support

Work with bigWig signals using ceasBW:

ceasBW -b peaks.bed -w signal.bw -g refGene.sqlite --name chip_bw

Site-centric profiling

Average enrichment around a set of regions:

sitepro -w signal.wig -b motifs.bed --span 1000 --step 20

For bigWig input use:

siteproBW -w signal.bw -b motifs.bed --span 1000 --step 20

siteproBW relies on the bx-python library for BigWig access. Install it with:

pip install bx-python

Gene-centered annotation only

Generate annotation without profiling:

gca -b peaks.bed -g refGene.sqlite --span 3000 --name gca_out

Build genome background annotation

Pre-compute genome background tables for use with CEAS:

./build_genomeBG.sh hg38

Each script supports --help for additional options.

License

The package is distributed under the Artistic License. See LICENSE.