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]>

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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'))

Peer review:

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 314 downloads 8 mentions 15 exports 3 dependencies

Last updated 2 months agofrom:d459b872fa. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 22 2024
R-4.5-winNOTEDec 22 2024
R-4.5-linuxNOTEDec 22 2024
R-4.4-winNOTEDec 22 2024
R-4.4-macNOTEDec 22 2024
R-4.3-winNOTEDec 22 2024
R-4.3-macNOTEDec 22 2024

Exports:drawMA_volecdfAUCequalSpaceexactNBtest1getAdjustDispgetNormFactorgetQgetTgetTgroupnbinomTestForMatricesSHnbTestSHplotDispersionrnbinomMVrowVarssim

Dependencies:bitopscaToolsRColorBrewer

sSeq

Rendered fromsSeq.Rnwusingutils::Sweaveon Dec 22 2024.

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