prebs
Probe region expression estimation for RNA-seq data for improved microarray comparability
Bioconductor version: Release (2.12)
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>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("prebs")
To cite this package in a publication, start R and enter:
citation("prebs")
Documentation
| R Script | prebs User Guide | |
| Reference Manual |
Details
| biocViews | Bioinformatics, GeneExpression, Microarray, Preprocessing, RNAseq, Sequencing, Software |
| Version | 1.0.2 |
| In Bioconductor since | BioC 2.13 (R-2.18) |
| License | Artistic-2.0 |
| Depends | R (>= 2.14.0), Rsamtools, affy |
| Imports | parallel, methods, stats, GenomicRanges, IRanges |
| Suggests | prebsdata, hgu133plus2cdf, hgu133plus2probe |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Downloads
| Package Source | prebs_1.0.2.tar.gz |
| Windows Binary | prebs_1.0.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | prebs_1.0.2.tgz |
| Package Downloads Report | Download Stats |
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