Main logo
tutorial arrow
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.


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.

User report

tutorial arrow
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community

0 user reviews

0 user reviews

No review has been posted.

RIPSeeker forum

tutorial arrow
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

No open topic.

RIPSeeker classification

RIPSeeker specifications

Software type:
Restrictions to use:
Operating system:
Unix/Linux, Mac OS, Windows
GNU General Public License version 2.0
methods, S4Vectors, IRanges, GenomicRanges, SummarizedExperiment, Rsamtools, GenomicAlignments, rtracklayer
Command line interface
Input format:
Programming languages:
Computer skills:

RIPSeeker distribution


tutorial arrow
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

RIPSeeker support



tutorial arrow
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship



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

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.