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Bioconductor - prebs (development version)

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 (3.22)

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 "4.5") 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")
Details biocViews GeneExpression, ImmunoOncology, Microarray, Preprocessing, RNASeq, Sequencing, Software Version 1.49.0 In Bioconductor since BioC 2.12 (R-3.0) (12.5 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 System Requirements URL See More Package Archives

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

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