RIPSeeker

DOI: 10.18129/B9.bioc.RIPSeeker    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RIPSeeker.

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

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("RIPSeeker")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.24.0
In Bioconductor since	BioC 2.12 (R-3.0) (6.5 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
Links To Me
Build Report

Package Archives

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

Source Package	RIPSeeker_1.24.0.tar.gz
Windows Binary	RIPSeeker_1.24.0.zip
Mac OS X 10.11 (El Capitan)	RIPSeeker_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RIPSeeker
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RIPSeeker
Package Short Url	https://bioconductor.org/packages/RIPSeeker/
Package Downloads Report	Download Stats