tweeDEseq
This is the released version of tweeDEseq; for the devel version, see tweeDEseq.
RNA-seq data analysis using the Poisson-Tweedie family of distributions
Bioconductor version: Release (3.23)
Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.
Author: Dolors Pelegri-Siso [aut, cre]
, Juan R. Gonzalez [aut]
, Mikel Esnaola [aut], Robert Castelo [aut]
Maintainer: Dolors Pelegri-Siso <dolors.pelegri at isglobal.org>
citation("tweeDEseq")):
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")
BiocManager::install("tweeDEseq")
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("tweeDEseq")| tweeDEseq: analysis of RNA-seq data using the Poisson-Tweedie family of distributions | R Script | |
| Reference Manual |
Details
| biocViews | DNASeq, DifferentialExpression, ImmunoOncology, RNASeq, Sequencing, Software, StatisticalMethod |
| Version | 1.58.0 |
| In Bioconductor since | BioC 2.9 (R-2.14) (15 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.3.0) |
| Imports | Rcpp (>= 1.0.10), MASS, limma, edgeR, parallel, cqn, grDevices, graphics, stats, utils |
| System Requirements | |
| URL | https://github.com/isglobal-brge/tweeDEseq/ |
| Bug Reports | https://github.com/isglobal-brge/tweeDEseq/issues |
See More
| Suggests | tweeDEseqCountData, xtable |
| Linking To | Rcpp |
| Enhances | |
| Depends On Me | |
| Imports Me | ptmixed |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | tweeDEseq_1.58.0.tar.gz |
| Windows Binary (x86_64) | tweeDEseq_1.58.0.zip |
| macOS Binary (big-sur-x86_64) | tweeDEseq_1.58.0.tgz |
| macOS Binary (sonoma-arm64) | tweeDEseq_1.58.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/tweeDEseq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/tweeDEseq |
| Bioc Package Browser | https://code.bioconductor.org/browse/tweeDEseq/ |
| Package Short Url | https://bioconductor.org/packages/tweeDEseq/ |
| Package Downloads Report | Download Stats |