ANCOMBC

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ANCOMBC.

Analysis of compositions of microbiomes with bias correction


Bioconductor version: 3.14

ANCOMBC is a package for normalizing the microbial observed abundance data due to unequal sampling fractions across samples, and identifying taxa (e.g. phyla, families, genera, species, etc.) that are differentially abundant with respect to the covariate of interest (e.g. study groups) between two or more groups of multiple samples.

Author: Huang Lin [cre, aut] , Shyamal Das Peddada [aut]

Maintainer: Huang Lin <HUL40 at pitt.edu>

Citation (from within R, enter citation("ANCOMBC")):

Installation

To install this package, start R (version "4.1") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ANCOMBC")

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("ANCOMBC")
ANCOMBC HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, Microbiome, Normalization, Sequencing, Software
Version 1.4.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License Artistic-2.0
Depends
Imports stats, MASS, nloptr, Rdpack, phyloseq, microbiome
System Requirements
URL https://github.com/FrederickHuangLin/ANCOMBC
Bug Reports https://github.com/FrederickHuangLin/ANCOMBC/issues
See More
Suggests knitr, tidyverse, testthat, DT, magrittr, qwraps2 (>= 0.5.0), rmarkdown
Linking To
Enhances
Depends On Me
Imports Me microbiomeMarker
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ANCOMBC_1.4.0.tar.gz
Windows Binary ANCOMBC_1.4.0.zip
macOS 10.13 (High Sierra) ANCOMBC_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ANCOMBC
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ANCOMBC
Bioc Package Browser https://code.bioconductor.org/browse/ANCOMBC/
Package Short Url https://bioconductor.org/packages/ANCOMBC/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.14 Source Archive