R package CSSP

This page provides download links to an R package for power computations of ChIP-seq experiments. The method is described in:

Zuo, C. and Keles, S. (2012), A Statistical Framework for Power Calculations in ChIP-Seq Experiments", Bioinformatics.

CSSP is currently available through Bioconductor.org.


Latest version: CSSP-0.99

    We have submitted this version to bioconductor. This version is compatible with R-3.0 .

version 1.4

Updates in this version:
  • Enabling genome wide model fitting and power computation. Users may refer to the added "useGrid" and "nsize" parameters in the "cssp.fit" function.
  • Changing slotnames "beta" and "alpha" to "b" and "a" in the "bayesBindFit" class.

version 1.2

This package enables:
  • Constructing bin-level data from aligned short reads;
  • Fitting the proposed local Poisson model for ChIP-seq data;
  • Calculating power at desired FDR and effect sizes.

Installation instructions

  • From Biocondutor, within R: source("http://bioconductor.org/biocLite.R"); biocLite("CSSP") .
  • Using source package, within R: install.packages("path/CSSP_0.99.tar.gz", repo = NULL, type = "source", dependencies = TRUE), where path is the path to the package.
  • Outside R: R CMD INSTALL CSSP_0.99.tar.gz


Please join our CSSP google group for more downloads information, questions and feedbacks. You may also contact zuo AT stat.wisc.edu