ANCOMBC

DOI: 10.18129/B9.bioc.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>

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")

 

HTML	R Script	ANCOMBC
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, Microbiome, Normalization, Sequencing, Software
Version	1.4.0
In Bioconductor since	BioC 3.12 (R-4.0) (1.5 years)
License	Artistic-2.0
Depends
Imports	stats, MASS, nloptr, Rdpack, phyloseq, microbiome
LinkingTo
Suggests	knitr, tidyverse, testthat, DT, magrittr, qwraps2 (>= 0.5.0), rmarkdown
SystemRequirements
Enhances
URL	https://github.com/FrederickHuangLin/ANCOMBC
BugReports	https://github.com/FrederickHuangLin/ANCOMBC/issues
Depends On Me
Imports Me	microbiomeMarker
Suggests Me
Links To Me
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
Package Short Url	https://bioconductor.org/packages/ANCOMBC/
Package Downloads Report	Download Stats