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("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 |
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 |