RIPSeeker

DOI: 10.18129/B9.bioc.RIPSeeker    

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see RIPSeekerData.

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

Bioconductor version: Release (3.11)

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 "4.0") 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

PDF		Reference Manual

Details

biocViews	RIPSeq, Sequencing, Software
Version	1.28.0
In Bioconductor since	BioC 2.12 (R-3.0) (7.5 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
Windows Binary
macOS 10.13 (High Sierra)
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