prebs

DOI: 10.18129/B9.bioc.prebs    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see prebs.

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

Bioconductor version: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

PDF	R Script	prebs User Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	GeneExpression, ImmunoOncology, Microarray, Preprocessing, RNASeq, Sequencing, Software
Version	1.32.0
In Bioconductor since	BioC 2.12 (R-3.0) (8.5 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
Links To Me
Build Report

Package Archives

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

Source Package	prebs_1.32.0.tar.gz
Windows Binary	prebs_1.32.0.zip
macOS 10.13 (High Sierra)	prebs_1.32.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/prebs
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/prebs
Package Short Url	https://bioconductor.org/packages/prebs/
Package Downloads Report	Download Stats