RIPSeeker

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

Bioconductor version: Release (2.12)

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	HighThroughputSequencing, RIPseq, Software
Version	1.0.0
In Bioconductor since	BioC 2.13 (R-2.18)
License	GPL-2
Depends	R (>= 2.15), methods, IRanges, GenomicRanges, rtracklayer, Rsamtools
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_1.0.0.tar.gz
Windows Binary	RIPSeeker_1.0.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	RIPSeeker_1.0.0.tgz
Package Downloads Report	Download Stats

Workflows »

Common Bioconductor workflows include:

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Hosting provided by Fred Hutchinson Cancer Research Center