Bioconductor – 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>

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

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")

 

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Negative Binomial Additive Model for RNA-Seq Data
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Details

biocViews Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software
Version 1.0.1
In Bioconductor since BioC 3.9 (R-3.6) (
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 github.com/reese3928/NBAMSeq
BugReports github.com/reese3928/NBAMSeq/issues
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