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sSeq

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

Bioconductor version: Release (3.17)

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 (from within R, enter citation("sSeq")):

Installation

To install this package, start R (version "4.3") 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 PDF R Script
Reference Manual PDF

Details

biocViews ImmunoOncology, RNASeq, Software
Version 1.38.0
In Bioconductor since BioC 2.13 (R-3.0) (10 years)
License GPL (>= 3)
Depends R (>= 3.0), caTools, RColorBrewer
Imports
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Depends On Me
Imports Me MLSeq
Suggests Me NBLDA
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package sSeq_1.38.0.tar.gz
Windows Binary sSeq_1.38.0.zip
macOS Binary (x86_64) sSeq_1.38.0.tgz
macOS Binary (arm64) sSeq_1.38.0.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