Welcome
This is a site for an improved version of the spp package, initially developed by Dr. Peter Kharchenko, for analyzing ChIP-Seq data. For more details about the biological background and computation methods employed for calling binding positions, please refer to [1].
Features
The motivation of developing a new version of spp is to improve the original spp package such that it can meet current user requests and cope with new challenges. Compared to the original spp package, the new version will be improved in the following aspects:
- Restructuring the core design based on reference class
- Expanding functionalities such as quality control and dealing with replicates
- Improving the visualization, importing and exporting functionalities
- Enhancing the efficiency of parallel computing using multicore
- Optimizing memory control to minimize memory usage
- Enabling real-time computing upon visualization of profiles
Installation
The new spp package complies with the bioconductor format, and will be submitted to bioconductor soon. In the future, just use 'biocLite' to install this package. For now, it can only be installed as a source package, so either use 'install.package' inside R or 'R CMD INSTALL' in command line.
Note that no matter how you want to install spp, please pre-install boost c++ in order to compile the embedded c++ code.
Guide for the User and Contributor
A step-by-step user guide demonstrating how to use spp on ENCODE sample data sets is available here. For more information about the design of the package, please refer to the guide for contributors
Developer team and contributors
Xin Wang, Francesco Ferrari, Nils Gehlenborg, Luca Petiti and Peter Kharchenko (PI)
Contact
Please contact Xin Wang (xin_wang@hms.harvard.edu) or Peter Kharchenko (peter.kharchenko@post.harvard.edu) if you have any comments, suggestions or find any bug in the package.
REFERENCES
[1] 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