recipe bioconductor-sseq

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

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/sSeq.html

License:

GPL (>= 3)

Recipe:

/bioconductor-sseq/meta.yaml

Links:

biotools: sseq, doi: 10.1093/bioinformatics/btt143

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.

package bioconductor-sseq

Versions:

1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0, 

1.36.0-0,  1.32.0-0,  1.30.0-0,  1.28.0-1,  1.28.0-0,  1.26.0-0,  1.24.0-0,  1.22.0-1,  1.22.0-0,  1.20.1-0,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-0

Depends:

• r-base >=4.2,<4.3.0a0

• r-catools

• r-rcolorbrewer

Required By:

• bioconductor-mlseq

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-sseq

and update with:

conda update bioconductor-sseq

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-sseq:<tag>

(see bioconductor-sseq/tags for valid values for <tag>)

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