prebs

This is the released version of prebs; for the devel version, see prebs.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12

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

Bioconductor version: Release (3.23)

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")):

Karolis Uziela and Antti Honkela. prebs: Probe region expression estimation for RNA-seq data for improved microarray comparability. doi:10.18129/B9.bioc.prebs, R package version 1.52.0, https://bioconductor.org/packages/prebs.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

prebs User Guide	PDF	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	GeneExpression, ImmunoOncology, Microarray, Preprocessing, RNASeq, Sequencing, Software
Version	1.52.0
In Bioconductor since	BioC 2.12 (R-3.0) (13.5 years)
License	Artistic-2.0
Depends	R (>= 2.14.0), GenomicAlignments, affy, RPA
Imports	parallel, methods, stats, GenomicRanges (>= 1.13.3), IRanges, Biobase, Seqinfo, S4Vectors
System Requirements
URL

Suggests	prebsdata, hgu133plus2cdf, hgu133plus2probe
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	prebs_1.52.0.tar.gz
Windows Binary (x86_64)	prebs_1.52.0.zip
macOS Binary (big-sur-x86_64)	prebs_1.52.0.tgz
macOS Binary (sonoma-arm64)	prebs_1.52.0.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