sSeq
Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Bioconductor version: Release (3.19)
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.
Author: Danni Yu <dyu at purdue.edu>, Wolfgang Huber <whuber at embl.de> and Olga Vitek <ovitek at purdue.edu>
Maintainer: Danni Yu <dyu at purdue.edu>
citation("sSeq")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("sSeq")
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("sSeq")| sSeq | R Script | |
| Reference Manual |
Details
| biocViews | ImmunoOncology, RNASeq, Software |
| Version | 1.42.0 |
| In Bioconductor since | BioC 2.13 (R-3.0) (11 years) |
| License | GPL (>= 3) |
| Depends | R (>= 3.0), caTools, RColorBrewer |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | MLSeq |
| Suggests Me | NBLDA |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | sSeq_1.42.0.tar.gz |
| Windows Binary (x86_64) | sSeq_1.42.0.zip |
| macOS Binary (x86_64) | sSeq_1.42.0.tgz |
| macOS Binary (arm64) | sSeq_1.42.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/sSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/sSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/sSeq/ |
| Package Short Url | https://bioconductor.org/packages/sSeq/ |
| Package Downloads Report | Download Stats |