NBAMSeq

DOI: 10.18129/B9.bioc.NBAMSeq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see NBAMSeq.

Negative Binomial Additive Model for RNA-Seq Data

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

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

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")

 

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

Details

biocViews	Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version	1.0.1
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-2
Depends	R (>= 3.6), SummarizedExperiment, S4Vectors
Imports	DESeq2, mgcv (>= 1.8-24), BiocParallel, genefilter, methods, stats
LinkingTo
Suggests	knitr, rmarkdown, testthat, ggplot2
SystemRequirements
Enhances
URL	https://github.com/reese3928/NBAMSeq
BugReports	https://github.com/reese3928/NBAMSeq/issues
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	NBAMSeq_1.0.1.tar.gz
Windows Binary	NBAMSeq_1.0.1.zip
Mac OS X 10.11 (El Capitan)	NBAMSeq_1.0.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/NBAMSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/NBAMSeq
Package Short Url	https://bioconductor.org/packages/NBAMSeq/
Package Downloads Report	Download Stats