Software
Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation. You can download and install RIPSeeker from Bioconductor.
PIIKA: Platform for Integrated, Intelligent Kinome Analysis
PIIKA is a software pipeline implemented in R for analyzing data from kinome microarrays. I do not maintain this software. If you wish to use PIIKA for academic, non-commercial purposes, please e-mail here to obtain a license form.
