prebs
Probe region expression estimation for RNA-seq data for improved microarray comparability
Bioconductor version: Release (3.17)
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("prebs")):
Installation
To install this package, start R (version "4.3") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, ImmunoOncology, Microarray, Preprocessing, RNASeq, Sequencing, Software |
| Version | 1.40.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (10.5 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 |
| Linking To | |
| Suggests | prebsdata, hgu133plus2cdf, hgu133plus2probe |
| System Requirements | |
| Enhances | |
| URL |
See More
| 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_1.40.0.tar.gz |
| Windows Binary | prebs_1.40.0.zip (64-bit only) |
| macOS Binary (x86_64) | prebs_1.40.0.tgz |
| macOS Binary (arm64) | prebs_1.40.0.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 |