README.md

In chandlerzuo/cssp: ChIP-Seq Statistical Power

CSSP: ChIP-SEQ Statistical Power

What is CSSP?

CSSP (ChIP-SEQ Statistical Power) is a statistical framework for computing the power of detecting enriched regions for ChIP-SEQ experiments.

How does it Work?

CSSP framework incorporates the following steps:

• Constructing bin-level data from aligned short reads for both a ChIP sample and a control sample;
• Preparing bin-level genome mappability and gc-content scores;
• Fitting the proposed local Poisson model for the bin-level sequencing data;
• Calculating power at desired FDR and effect sizes.

Installation

CSSP is currently available in bioconductor. A stable version can be accessed through Bioconductor by:

 source("http://cran.cnr.berkeley.edu")
 biocLite("CSSP")

References

Zuo, C. and Keles, S., A Statistical Framework for Power Calculations in ChIP-Seq Experiments, Bioinformatics(2013) doi: 10.1093/bioinformatics/btt200

Acknowledgement

CSSP is developed by Keles Lab at University of Wisconsin Madison.

chandlerzuo/cssp documentation built on May 13, 2019, 3:23 p.m.