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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.

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RIPSeeker classification

RIPSeeker specifications

Software type:
Package/Module
Restrictions to use:
None
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.12.0
Requirements:
methods, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, Rsamtools, GenomicAlignments, rtracklayer
Interface:
Command line interface
Input format:
SAM, BAM, BED
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes

RIPSeeker distribution

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No versioning.

RIPSeeker support

Documentation

Credits

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Publications

Institution(s)

Department of Computer Science, University of Toronto, Toronto, ON, Canada; The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada

Funding source(s)

Ontario Research Fund - Global Leader (Round 2); Natural Sciences and Engineering Research Council (NSERC) [327612]; NSERC Canada Graduate Scholarship and Ontario Graduate Scholarship

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