Package: tweeDEseq 1.53.0
Dolors Pelegri-Siso
tweeDEseq: RNA-seq data analysis using the Poisson-Tweedie family of distributions
Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.
Authors:
tweeDEseq_1.53.0.tar.gz
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tweeDEseq.pdf |tweeDEseq.html✨
tweeDEseq/json (API)
| # Install 'tweeDEseq' in R: |
| install.packages('tweeDEseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/isglobal-brge/tweedeseq/issues
- seizure - Epileptic seizure counts
On BioConductor:tweeDEseq-1.53.0(bioc 3.21)tweeDEseq-1.52.0(bioc 3.20)
immunooncologystatisticalmethoddifferentialexpressionsequencingrnaseqdnaseq
Last updated 22 days agofrom:3a20c3be2e. Checks:OK: 1 WARNING: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-aarch64 | WARNING | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-aarch64 | WARNING | Oct 31 2024 |
Exports:AIC.glmPTanova.glmPTcompareCountDistconfint.mlePTdPTexactTestPTfilterCountsformat.percgammratiogetParamgetZhuParamglmPTglmPT.fitgofTesthou2puigkk3kappa3kvectorLlogLik.glmPTlogLik.mlePTloglikGlmloglikGlmPTloglikPoissonTweedieloglikPoissonTweedie2loglikPoissonTweedie3logprobsMAplotMAplot.tweeDEmlePoissonTweediemomentEstimatesmomentEstimates_wt_CnormalizeCountsnprobspermtestprint.glmPTprint.mlePTprint.tweeDEpuig2houqqchisqrPTshapeTrendsummary.glmPTtestPoissonTweedietestShapePTtweeDEtweeDEglmtweeDExactVplotVplot.tweeDEzhu2houzhuprobs
Dependencies:cqnedgeRlatticelimmalocfitMASSMatrixMatrixModelsmclustnor1mixquantregRcppSparseMstatmodsurvival
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compare count data distributions | compareCountDist |
| The Poisson-Tweedie family of distributions | dPT rPT |
| Count data filtering | filterCounts |
| Fit Poisson-Tweedie generalized linear model. | glmPT tweeDEglm |
| Test the goodness of fit of every row in a matrix of counts | gofTest |
| Methods for objects of class 'mlePT' | confint.mlePT logLik.mlePT print.mlePT |
| Maximum likelihood estimation of the Poisson-Tweedie parameters | getParam mlePoissonTweedie mlePT |
| Count data normalization | normalizeCounts |
| Chi-square quantile-quantile plot | qqchisq |
| Epileptic seizure counts | seizure |
| Test shape parameter of PT | testShapePT |
| Score test for differences between two Poisson-Tweedie groups | MAplot MAplot.tweeDE print.tweeDE testPoissonTweedie tweeDE Vplot Vplot.tweeDE |
| Exact test for differences between two Poisson-Tweedie groups | exactTestPT tweeDExact |
