sSeq
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Bioconductor version: 3.23 · Package version: 1.50.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sSeq")Details
| Maintainer | Danni Yu <dyu@purdue.edu> |
| Author | Danni Yu <dyu@purdue.edu>, Wolfgang Huber <whuber@embl.de> and Olga Vitek <ovitek@purdue.edu> |
| License | GPL (>= 3) |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | ImmunoOncology, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/sSeq/ |
Citation
From within R, enter citation("sSeq"):
Danni Yu, Wolfgang Huber and Olga Vitek. sSeq: Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size. doi:10.18129/B9.bioc.sSeq, R package version 1.50.0, https://bioconductor.org/packages/sSeq.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | sSeq_1.50.0.tar.gz |
| Windows binary (x86_64) | sSeq_1.50.0.zip |
| macOS binary (arm64) | sSeq_1.50.0.tgz |
| macOS binary (x86_64) | sSeq_1.50.0.tgz |
Dependencies
Depends: R (>= 3.0), caTools, RColorBrewer