- Home
- Bioconductor 3.1
- Software Packages
- RIPSeeker
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("RIPSeeker")
In most cases, you don't need to download the package archive at all.
RIPSeeker
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
Bioconductor version: 3.1
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 and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("RIPSeeker")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RIPSeeker")
| R Script | RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | RIPSeq, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (2.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.15), methods, IRanges, GenomicRanges, 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 | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | RIPSeeker_1.8.0.tar.gz |
| Windows Binary | RIPSeeker_1.8.0.zip |
| Mac OS X 10.6 (Snow Leopard) | RIPSeeker_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | RIPSeeker_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/RIPSeeker/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/RIPSeeker/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
