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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Coverage, DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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_1.29.0.tar.gz |
| Windows Binary (x86_64) | NBAMSeq_1.29.0.zip |
| macOS Binary (big-sur-x86_64) | NBAMSeq_1.29.0.tgz |
| macOS Binary (sonoma-arm64) | NBAMSeq_1.29.0.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 |