- Home
- Bioconductor 2.8
- Software Packages
- rnaSeqMap
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rnaSeqMap")
In most cases, you don't need to download the package archive at all.
rnaSeqMap
|
This package is for version 2.8 of Bioconductor; for the stable, up-to-date release version, see rnaSeqMap.
rnaSeq analyses using xmapcore database
Bioconductor version: 2.8
Provides means of analysis for RNAseq data, used together with genomic annotation from Ensembl. Requires a set of BAM files on the input or alternatively, an xmapcore database in MySQL as a back-end, which is also a storage for sequencing reads. Front-end analyses include transformations of the coverage function, splicing analysis, finding irreducible regions with the two-sliding-windows algorithm and genomic region visualizations.
Author: Anna Lesniewska <alesniewska at cs.put.poznan.pl>; Michal Okoniewski <michal at fgcz.ethz.ch>
Maintainer: Michal Okoniewski <michal at fgcz.ethz.ch>
Citation (from within R,
enter citation("rnaSeqMap")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("rnaSeqMap")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("rnaSeqMap")
| rnaSeqMap.pdf | ||
| Reference Manual |
Details
| biocViews | Annotation, Bioinformatics, DifferentialExpression, GeneExpression, HighThroughputSequencing, RNAseq, ReportWriting, SAGE, Software, Transcription, Visualization |
| Version | 2.7.12 |
| In Bioconductor since | BioC 2.7 (R-2.12) (5.5 years) |
| License | GPL-2 |
| Depends | R (>= 2.11.0), methods, xmapcore, Biobase, Rsamtools |
| Imports | GenomicRanges, IRanges, edgeR, DESeq, DBI, RMySQL (>= 0.6-0) |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | rnaSeqMap_2.7.12.tar.gz |
| Windows Binary | rnaSeqMap_2.7.12.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | |
| Mac OS X 10.9 (Mavericks) | |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/rnaSeqMap/tree/release-2.8 |
| Package Short Url | http://bioconductor.org/packages/rnaSeqMap/ |
| 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
