Package: sSeq 1.45.0

Danni Yu

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

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.

Authors:Danni Yu <[email protected]>, Wolfgang Huber <[email protected]> and Olga Vitek <[email protected]>

sSeq_1.45.0.tar.gz
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sSeq.pdf |sSeq.html
sSeq/json (API)

# Install 'sSeq' in R:
install.packages('sSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:sSeq-1.45.0(bioc 3.21)sSeq-1.44.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologyrnaseq

4.98 score 2 packages 4 scripts 338 downloads 8 mentions 15 exports 3 dependencies

Last updated 4 months agofrom:d459b872fa. Checks:1 OK, 6 NOTE. Indexed: yes.

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Doc / VignettesOKJan 21 2025
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R-4.3-winNOTEJan 21 2025
R-4.3-macNOTEJan 21 2025

Exports:drawMA_volecdfAUCequalSpaceexactNBtest1getAdjustDispgetNormFactorgetQgetTgetTgroupnbinomTestForMatricesSHnbTestSHplotDispersionrnbinomMVrowVarssim

Dependencies:bitopscaToolsRColorBrewer

sSeq

Rendered fromsSeq.Rnwusingutils::Sweaveon Jan 21 2025.

Last update: 2013-11-01
Started: 2013-11-01