To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("RIPSeeker")

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

RIPSeeker

DOI: 10.18129/B9.bioc.RIPSeeker    

This is the development version of RIPSeeker; for the stable release version, see RIPSeeker.

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

Bioconductor version: Development (3.6)

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:

## try http:// if https:// URLs are not supported
source("https://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 1.17.0
In Bioconductor since BioC 2.12 (R-3.0) (4.5 years)
License GPL-2
Depends R (>= 2.15), methods, S4Vectors(>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment, Rsamtools, GenomicAlignments, rtracklayer
Imports
LinkingTo
Suggests biomaRt, ChIPpeakAnno, parallel, GenomicFeatures
SystemRequirements
Enhances
URL http://www.cs.utoronto.ca/~yueli/software.html
Depends On Me RIPSeekerData
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source RIPSeeker_1.17.0.tar.gz
Windows Binary RIPSeeker_1.17.0.zip
Mac OS X 10.11 (El Capitan) RIPSeeker_1.17.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/RIPSeeker
Package Short Url http://bioconductor.org/packages/RIPSeeker/
Package Downloads Report Download Stats

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