RIPSeeker

RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

Bioconductor version: Development (3.0)

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.

Author: Yue Li

Maintainer: Yue Li <yueli at cs.toronto.edu>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("RIPSeeker")

To cite this package in a publication, start R and enter:

    citation("RIPSeeker")

Documentation

PDF R Script RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
PDF   Reference Manual
Text   NEWS

Details

biocViews RIPSeq, Sequencing, Software
Version 1.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License GPL-2
Depends R (>= 2.15), methods, IRanges, GenomicRanges, Rsamtools, GenomicAlignments, rtracklayer
Imports
Suggests biomaRt, ChIPpeakAnno, parallel, GenomicFeatures
System Requirements
URL http://www.cs.utoronto.ca/~yueli/software.html
Depends On Me RIPSeekerData
Imports Me
Suggests Me

Package Downloads

Package Source RIPSeeker_1.5.0.tar.gz
Windows Binary RIPSeeker_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) RIPSeeker_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
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