Introduction | Advantages of DiPPER | Benchmarking results against alternative methods | More information | Installation | Stan backend (cmdstanr) | Bioconductor dependencies and DiPPER | Quick start | More complex example | Input data and other settings | Type of abundance data | Controlling for sequencing (read) depth | Symmetric or asymmetric hierarchical prior | Session Information
Package: DiPPER 0.99.1
Juho Pelto
DiPPER: Differential Prevalence via Probabilistic Estimation in R
Implements a Bayesian hierarchical model for differential prevalence analysis, tailored for microbiome studies. The method accommodates both cross-sectional and longitudinal designs, providing finite effect estimates and uncertainty intervals that are naturally adjusted for multiple testing via hierarchical shrinkage. Posterior inference is performed via Markov chain Monte Carlo (MCMC) using 'CmdStan' as the backend.
Authors:
DiPPER_0.99.1.tar.gz
DiPPER_0.99.1.zip(r-4.7-x86_64)DiPPER_0.99.1.zip(r-4.7-arm64)DiPPER_0.99.1.zip(r-4.6-x86_64)DiPPER_0.99.1.zip(r-4.6-arm64)DiPPER_0.99.1.zip(r-4.5-x86_64)
DiPPER_0.99.1.tgz(r-4.6-x86_64)DiPPER_0.99.1.tgz(r-4.6-arm64)DiPPER_0.99.1.tgz(r-4.5-x86_64)DiPPER_0.99.1.tgz(r-4.5-arm64)
DiPPER_0.99.1.tar.gz(r-4.7-arm64)DiPPER_0.99.1.tar.gz(r-4.7-x86_64)DiPPER_0.99.1.tar.gz(r-4.6-arm64)DiPPER_0.99.1.tar.gz(r-4.6-x86_64)
DiPPER_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DiPPER/json (API)
| # Install 'DiPPER' in R: |
| install.packages('DiPPER', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jepelt/dipper/issues
Datasets:
- fit_example - Example DiPPER model fit object
- tse_hintikka - Gut microbiome dataset from Hintikka et al.
- VatanenT_2016_subset - Longitudinal gut microbiome dataset from Vatanen et al.
softwaremicrobiomebayesianregressiondifferentialexpressionsequencingbioconductorpresence-absence-matrixstan
Last updated from:657a071a85. Checks:1 NOTE, 15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 175 | ||
| linux-devel-arm64 | OK | 250 | ||
| linux-devel-x86_64 | OK | 408 | ||
| source / vignettes | OK | 281 | ||
| linux-release-arm64 | OK | 266 | ||
| linux-release-x86_64 | OK | 358 | ||
| macos-release-arm64 | OK | 189 | ||
| macos-release-x86_64 | OK | 355 | ||
| macos-oldrel-arm64 | OK | 305 | ||
| macos-oldrel-x86_64 | OK | 668 | ||
| windows-devel-arm64 | OK | 351 | ||
| windows-devel-x86_64 | OK | 268 | ||
| windows-release-arm64 | OK | 368 | ||
| windows-release-x86_64 | OK | 253 | ||
| windows-oldrel-x86_64 | OK | 257 | ||
| wasm-release | OK | 137 |
Exports:dipper
Dependencies:abindapeBHBiobaseBiocGenericsBiocParallelBiostringscallrclicodetoolscpp11crayonDelayedArraydigestdplyrfarverformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggplot2gluegtableinstantiateIRangesisobandjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsnlmeotelpillarpkgconfigprocessxpspurrrR6rappdirsRColorBrewerRcpprlangS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraystringistringrSummarizedExperimenttibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentutf8vctrsviridisLitewithrXVectoryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| DiPPER (Differential Prevalence via Probabilistic Estimation in R) | dipper |
| Pre-computed DiPPER fits | DiPPER-extdata fit_hintikka fit_vatanen |
| Example DiPPER model fit object | fit_example |
| Plot method for DiPPER fit objects | plot.dipper_fit |
| Print a summary of a DiPPER model fit | print.dipper_fit |
| Summarize DiPPER results for the variable of interest | summary.dipper_fit |
| Gut microbiome dataset from Hintikka et al. (2021) | tse_hintikka |
| Longitudinal gut microbiome dataset from Vatanen et al. (2016) | VatanenT_2016_subset |