Thank you for using spp!
-
This is an improved version of the original spp package developed by Dr. Peter Kharchenko. To review the original spp package and its features, check the manual at http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutorial.html. To understand more about the biological background and computational methods, please refer to: Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol. 2008 Dec;26(12):1351-9.
-
For more detailed introduction of features of this package, please go to: http://xinwang2hms.github.io/SPP
-
Before installing spp, please make sure that Boost c++ is already pre-installed.
-
To install spp, you may either use 'R CMD INSTALL spp_0.0.1.tar.gz' in command line or 'install.packages("spp_0.0.1.tar.gz", type="source")' in R console.
-
Please go to the wiki site: https://github.com/xinwang2hms/SPP/wiki to find a demonstration of ChIP-seq data analysis on ENCODE data sets.
-
The current spp has only been tested on Ubuntu linux. We are now testing on Mac OS and Windows.
-
Please contact xin_wang@hms.harvard.edu to report bugs! We are also open to comments and suggestions.