To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("prebs")
In most cases, you don't need to download the package archive at all.
prebs
|
Probe region expression estimation for RNA-seq data for improved microarray comparability
Bioconductor version: 3.2
The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.
Author: Karolis Uziela and Antti Honkela
Maintainer: Karolis Uziela <karolis.uziela at scilifelab.se>
Citation (from within R,
enter citation("prebs")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("prebs")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("prebs")
| prebs User Guide | ||
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, Microarray, Preprocessing, RNASeq, Sequencing, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 years) |
| License | Artistic-2.0 |
| Depends | R (>= 2.14.0), GenomicAlignments, affy, RPA |
| Imports | parallel, methods, stats, GenomicRanges(>= 1.13.3), IRanges, Biobase, GenomeInfoDb, S4Vectors |
| LinkingTo | |
| Suggests | prebsdata, hgu133plus2cdf, hgu133plus2probe |
| 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 | prebs_1.10.0.tar.gz |
| Windows Binary | prebs_1.10.0.zip |
| Mac OS X 10.6 (Snow Leopard) | prebs_1.10.0.tgz |
| Mac OS X 10.9 (Mavericks) | prebs_1.10.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/prebs/tree/release-3.2 |
| Package Short Url | http://bioconductor.org/packages/prebs/ |
| 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
