ChIP-seq processing pipeline

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.