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.
Releases
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
Vignette
|