Getting started | Normalization and filtering | The Poisson-Tweedie family of distributions to model RNA-seq count data | Goodness of fit to a count data distribution | Testing for differential expression | Visualizing the results | Assessing differential expression calling accuracy | Fitting generalized linear models (GLM) | Session info
Package: tweeDEseq 1.59.0
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_1.59.0.tar.gz
tweeDEseq_1.59.0.zip(r-4.7)tweeDEseq_1.59.0.zip(r-4.6)tweeDEseq_1.59.0.zip(r-4.5)
tweeDEseq_1.59.0.tgz(r-4.6-x86_64)tweeDEseq_1.59.0.tgz(r-4.6-arm64)tweeDEseq_1.59.0.tgz(r-4.5-x86_64)tweeDEseq_1.59.0.tgz(r-4.5-arm64)
tweeDEseq_1.59.0.tar.gz(r-4.7-arm64)tweeDEseq_1.59.0.tar.gz(r-4.7-x86_64)tweeDEseq_1.59.0.tar.gz(r-4.6-arm64)tweeDEseq_1.59.0.tar.gz(r-4.6-x86_64)
tweeDEseq_1.59.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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
Datasets:
- seizure - Epileptic seizure counts
On BioConductor:tweeDEseq-1.59.0(bioc 3.24)tweeDEseq-1.58.0(bioc 3.23)
immunooncologystatisticalmethoddifferentialexpressionsequencingrnaseqdnaseq
Last updated from:e54bd6c012. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 183 | ||
| linux-devel-arm64 | WARNING | 161 | ||
| linux-devel-x86_64 | WARNING | 260 | ||
| source / vignettes | OK | 591 | ||
| linux-release-arm64 | WARNING | 179 | ||
| linux-release-x86_64 | WARNING | 258 | ||
| macos-release-arm64 | WARNING | 188 | ||
| macos-release-x86_64 | WARNING | 204 | ||
| macos-oldrel-arm64 | WARNING | 114 | ||
| macos-oldrel-x86_64 | WARNING | 182 | ||
| windows-devel | WARNING | 131 | ||
| windows-release | WARNING | 162 | ||
| windows-oldrel | WARNING | 137 | ||
| wasm-release | OK | 164 |
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 |
