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RIPSeeker
Provides a comprehensive analytical suite for RIP-seq analysis, not only including predicting RIP regions with or without a control library but also processing alignments, automatic genomic annotation, visualization from UCSC browser, etc. As an overview, RIPSeeker consists of two major steps: probabilistic inference of RIP regions (HMM posterior decoding and parameter optimization) and significance test for the inferred RIP regions from HMM (Detect RIP regions). RIPSeeker is able to detect strand-specific RIP regions by running the same workflow on either plus and minus strand separately, making use of the strand-specific information retained in the original RIP-seq protocol. It also takes advantage of modern computational architecture equipped with multiple processors by treating each chromosome as an independent thread and computing multiple threads in parallel using mclapply from parallel R package.
PARCLIP_suite / PhotoActivatable-Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation
Allows to study RNA-RNA binding protein (RBP) interactions in human cell lines. PARCLIP_suite maps the sequence reads and calculates the T-to-C conversion frequency for each annotated category of RNA and read length. It permits to inform experimentalists about the quality of their experiments, and the annotation category of their crosslinked RNAs in order to guide downstream data and functional analysis.
CLIPSeqTools
A highly flexible computational suite that can perform analysis from raw sequencing data with minimal user input. CLIPSeqTools contains a wide array of tools to provide an in-depth view of CLIP-seq data sets. It supports extensive customization and promotes improvization, a critical virtue, since CLIP-seq analysis is rarely well defined a priori. CLIPSeqTools has applications for a wide range of analyses that will give an in depth view of the analysed dataset. Examples of such analyses are: genome read coverage, distribution of reads on genic elements, motif enrichment, relative position of reads of two datasets, differential gene counts, etc). To highlight CLIPSeqTools capabilities, we used the suite to analyze Ago-miRNA HITS-CLIP data sets that we prepared from human brains.
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