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NBAMSeq

This is the development version of NBAMSeq; for the stable release version, see NBAMSeq.

Negative Binomial Additive Model for RNA-Seq Data


Bioconductor version: Development (3.20)

High-throughput sequencing experiments followed by differential expression analysis is a widely used approach to detect genomic biomarkers. A fundamental step in differential expression analysis is to model the association between gene counts and covariates of interest. NBAMSeq a flexible statistical model based on the generalized additive model and allows for information sharing across genes in variance estimation.

Author: Xu Ren [aut, cre], Pei Fen Kuan [aut]

Maintainer: Xu Ren <xuren2120 at gmail.com>

Citation (from within R, enter citation("NBAMSeq")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("NBAMSeq")

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("NBAMSeq")
Negative Binomial Additive Model for RNA-Seq Data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version 1.21.0
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License GPL-2
Depends R (>= 3.6), SummarizedExperiment, S4Vectors
Imports DESeq2, mgcv (>= 1.8-24), BiocParallel, genefilter, methods, stats
System Requirements
URL https://github.com/reese3928/NBAMSeq
Bug Reports https://github.com/reese3928/NBAMSeq/issues
See More
Suggests knitr, rmarkdown, testthat, ggplot2
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Package Archives

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

Source Package NBAMSeq_1.21.0.tar.gz
Windows Binary NBAMSeq_1.21.0.zip (64-bit only)
macOS Binary (x86_64) NBAMSeq_1.21.0.tgz
macOS Binary (arm64) NBAMSeq_1.21.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NBAMSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NBAMSeq
Bioc Package Browser https://code.bioconductor.org/browse/NBAMSeq/
Package Short Url https://bioconductor.org/packages/NBAMSeq/
Package Downloads Report Download Stats