To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

RIPSeeker

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

Bioconductor version: Release (2.14)

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>

Citation (from within R, enter citation("RIPSeeker")):

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("RIPSeeker")

 

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 1.4.0
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 Archives

Follow Installation instructions to use this package in your R session.

Package Source RIPSeeker_1.4.0.tar.gz
Windows Binary RIPSeeker_1.4.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) RIPSeeker_1.4.0.tgz
Mac OS X 10.9 (Mavericks) RIPSeeker_1.4.0.tgz
Browse/checkout source (username/password: readonly)
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