A multi-threaded wrapper for processing multi-replicate, multi-condition ChIPSeq samples
ChIPSeq and related methods, such as ATACSeq and Cut-and-Run, is increasingly being used not just as a means of discovery ("where is my factor binding?") but also as an assay for experimental conditions ("how does my mutant affect factor X occupancy?"). Many traditional ChIPSeq programs are not necessarily well equipped to handle multiple replicates and/or sample conditions.
This is a wrapper application for processing ChIPSeq samples comprised of multiple biological replicas and/or multiple conditions in a manner to make comparisons as consistent and uniform as possible across samples.
For full documentation, including overview, usage guide, examples, and installation guide, see the Documentation pages.
This is a Perl package and may be built using the standard incantation.
perl Build.PL
./Build
./Build install
For detailed notes on accessory packages and dependencies, see the Installation guide.
Timothy J. Parnell, PhD
Cancer Bioinformatics Shared Resource
Huntsman Cancer Institute
University of Utah
Salt Lake City, UT, 84112
This package is free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0. For details, see the full text of the license in the file LICENSE.
This package is distributed in the hope that it will be useful, but it is provided "as is" and without any express or implied warranties. For details, see the full text of the license in the file LICENSE.