DiPPER
This is the development version of DiPPER; to use it, please install the devel version of Bioconductor.
Differential Prevalence via Probabilistic Estimation in R
Bioconductor version: Development (3.24)
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.
Author: Juho Pelto [aut, cre]
, Leo Lahti [aut]
, Research Council of Finland [fnd] (Strategic Research Council, decisions 372345 and 374944)
Maintainer: Juho Pelto <jepelt at utu.fi>
citation("DiPPER")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("DiPPER")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DiPPER")| Differential Prevalence Analysis with DiPPER | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Bayesian, DifferentialExpression, Microbiome, Regression, Sequencing, Software |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.6.0) |
| Imports | instantiate, SummarizedExperiment, TreeSummarizedExperiment, stats, utils, ggplot2 |
| System Requirements | CmdStan (https://mc-stan.org/users/interfaces/cmdstan) |
| URL | https://github.com/jepelt/DiPPER |
| Bug Reports | https://github.com/jepelt/DiPPER/issues |
See More
| Suggests | testthat (>= 3.1.5), knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DiPPER_0.99.1.tar.gz |
| Windows Binary (x86_64) | DiPPER_0.99.1.zip |
| macOS Binary (big-sur-x86_64) | DiPPER_0.99.1.tgz |
| macOS Binary (sonoma-arm64) | DiPPER_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DiPPER |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DiPPER |
| Bioc Package Browser | https://code.bioconductor.org/browse/DiPPER/ |
| Package Short Url | https://bioconductor.org/packages/DiPPER/ |
| Package Downloads Report | Download Stats |