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:
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')) |
- countsTable - An Example Simulation Data
- countsTable - An Example Simulation Data
- countsTable - An Example Simulation Data
- countsTable - An Example Simulation Data
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.
Last updated 23 days agofrom:d459b872fa. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | NOTE | Oct 31 2024 |
| R-4.3-mac | NOTE | Oct 31 2024 |
Exports:drawMA_volecdfAUCequalSpaceexactNBtest1getAdjustDispgetNormFactorgetQgetTgetTgroupnbinomTestForMatricesSHnbTestSHplotDispersionrnbinomMVrowVarssim
Dependencies:bitopscaToolsRColorBrewer
