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: 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>

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

Installation

To install this package, start R (version "4.0") and enter:


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

BiocManager::install("RIPSeeker")

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

Documentation

Reference Manual PDF

Details

biocViews RIPSeq, Sequencing, Software
Version 1.28.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License GPL-2
Depends R (>= 2.15), methods, S4Vectors(>= 0.9.25), IRanges, GenomicRanges, SummarizedExperiment, Rsamtools, GenomicAlignments, rtracklayer
Imports
System Requirements
URL http://www.cs.utoronto.ca/~yueli/software.html
See More
Suggests biomaRt, ChIPpeakAnno, parallel, GenomicFeatures
Linking To
Enhances
Depends On Me RIPSeekerData
Imports Me
Suggests Me
Links To Me
Build Report 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
Old Source Packages for BioC 3.11 Source Archive