ChIP-Seq Processing Pipeline

Analysis of ChIP-seq and other functional sequencing data [Kharchenko PV (2008) ].

An R package for analysis of ChIP-seq and other functional sequencing data. Please see package homepage for details.


A unix-flavored OS with R (>= 3.3.0) installed.


Since version 1.15.4 spp is available on CRAN and can be installed using the command

install.pacakges("spp", dependencies=TRUE)

Alternatively you can use modtools to install spp:

devtools::install_github('hms-dbmi/spp', build_vignettes = FALSE)


download a .tar.gz containing the latest release and use the standard R installation command, e.g.:

R CMD INSTALL spp_1.13.tar.gz

Note: Since version 1.15.4 the Boost headers are incorporated and linked taking advantage of BH package to avoid problems due to non-standard Boost libraries installation.


Reference manual

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1.16.0 by Peter Kharchenko, a year ago

Browse source code at

Authors: Peter K

Documentation:   PDF Manual  

GPL-2 license

Imports Rsamtools, caTools, parallel, graphics, stats

Depends on Rcpp

Suggests methods

Linking to Rcpp, BH

See at CRAN