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 (3.21)
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 "4.5") 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
| Reference Manual |
Details
| biocViews | GeneExpression, ImmunoOncology, Microarray, Preprocessing, RNASeq, Sequencing, Software |
| Version | 1.47.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11.5 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
| Suggests | prebsdata, hgu133plus2cdf, hgu133plus2probe |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |