macsR-package: Facilitate analysis of MACS results
In drmjc/macsR: Facilitate analysis of MACS results.

Description Details macsR from the commandline MACS version MACS installation on OSX 10.7.3 MACS installation on Ubuntu Author(s) References See Also

MACS (model based analysis for ChIP-Seq) is a popular program for converting ChIP-Seq reads into peaks. If produces a number of output files in a directory, which to my mind can be improved a little. This package imports MACS results, improves the result files, and annotates peaks with their nearest TSS and CpG island.

import.macs.peaks.file is used to import MACS results.

fix.macs.output is used to ‘fix’ or improve the usability of MACS results, particularly for the end user who wants to get genomic coordinates in UCSC-style strings, and get BED files of just the significant peaks.

annotate.macs.output is used to annotate peaks by their closest TSS or CpG island. This uses ChIPpeakAnno, and pre-built TSS and CpG-island definitions, the former are from Ensembl, and the latter are from UCSC.

I've included a few shell scripts inside the bin directory, which can help run this code in offline mode. You can add this to your PATH, eg on OSX: PATH=$PATH:/Library/Frameworks/R.framework/Resources/library/macsR/bin
do.macs.sh: run MACS on 1 or 2 input bam files, fix the output & annotate the peaks with nearest TSS and CpG island. Note there are only a subset of the macs14 options available.
fix.macs.sh: fix/improve the look of MACS results.
annotate.macs.sh: annotated MACS results with neares TSS and CpG islands. Note I always run this after running fix.macs.sh. I plan to allow you to add additional BED files for annotating peaks, though bedtools may be a better way to do this.

This package does not include macs, but it does expect macs14 to be installed & on your path.

Download the tar.gz: https://github.com/downloads/taoliu/MACS/MACS-1.4.1.tar.gz
unpack & install to home dir:
$ python setup.py install --user
copy binaries from ./bin to ~/bin/macs14 & make executable
Edit $HOME/.bashrc file:
export PATH=$PATH:~/bin/macs14
export PYTHONPATH=~/Library/Python/2.7/lib/python/site-packages:$PYTHONPATH