banocc
This is the released version of banocc; for the devel version, see banocc.
Bayesian ANalysis Of Compositional Covariance
Bioconductor version: Release (3.23)
BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`. It provides as output the `stanfit` object as well as posterior median and credible interval estimates for each correlation element.
Author: Emma Schwager [aut, cre], Curtis Huttenhower [aut]
Maintainer: George Weingart <george.weingart at gmail.com>, Curtis Huttenhower <chuttenh at hsph.harvard.edu>
citation("banocc")):
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")
BiocManager::install("banocc")
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("banocc")| BAnOCC (Bayesian Analysis of Compositional Covariance) | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | Bayesian, ImmunoOncology, Metagenomics, Software |
| Version | 1.36.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (9.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.1), rstan (>= 2.17.4) |
| Imports | coda (>= 0.18.1), mvtnorm, stringr |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, methods, testthat, 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 | banocc_1.36.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | banocc_1.36.0.tgz |
| macOS Binary (sonoma-arm64) | banocc_1.36.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/banocc |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/banocc |
| Bioc Package Browser | https://code.bioconductor.org/browse/banocc/ |
| Package Short Url | https://bioconductor.org/packages/banocc/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |