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prebs

This is the development version of prebs; for the stable release version, see prebs.

Probe region expression estimation for RNA-seq data for improved microarray comparability


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("prebs")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("prebs")
prebs User Guide PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneExpression, ImmunoOncology, Microarray, Preprocessing, RNASeq, Sequencing, Software
Version 1.43.0
In Bioconductor since BioC 2.12 (R-3.0) (11 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
System Requirements
URL
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Suggests prebsdata, hgu133plus2cdf, hgu133plus2probe
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package prebs_1.43.0.tar.gz
Windows Binary prebs_1.43.0.zip
macOS Binary (x86_64) prebs_1.43.0.tgz
macOS Binary (arm64) prebs_1.43.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/prebs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/prebs
Bioc Package Browser https://code.bioconductor.org/browse/prebs/
Package Short Url https://bioconductor.org/packages/prebs/
Package Downloads Report Download Stats