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("NBAMSeq")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| Negative Binomial Additive Model for RNA-Seq Data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software |
| Version | 1.0.1 |
| 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 |
| 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 | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/NBAMSeq/ |
| Package Short Url | https://bioconductor.org/packages/NBAMSeq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |