ANCOMBC

DOI: 10.18129/B9.bioc.ANCOMBC  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see ANCOMBC.

Microbiome differential abudance and correlation analyses with bias correction

Bioconductor version: 3.17

ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2), Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC), and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package are designed to correct these biases and construct statistically consistent estimators.

Author: Huang Lin [cre, aut]

Maintainer: Huang Lin <huanglinfrederick at gmail.com>

Installation

To install this package, start R (version "4.3") 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	ANCOM Tutorial
HTML	R Script	ANCOM-BC Tutorial
HTML	R Script	ANCOM-BC2 Tutorial
HTML	R Script	SECOM Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, Microbiome, Normalization, Sequencing, Software
Version	2.2.2
In Bioconductor since	BioC 3.12 (R-4.0) (3 years)
License	Artistic-2.0
Depends	R (>= 4.3.0)
Imports	mia(>= 1.6.0), stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils
LinkingTo
Suggests	dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr
SystemRequirements
Enhances
URL	https://github.com/FrederickHuangLin/ANCOMBC
BugReports	https://github.com/FrederickHuangLin/ANCOMBC/issues
Depends On Me
Imports Me	benchdamic, microbiomeMarker
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ANCOMBC_2.2.2.tar.gz
Windows Binary	ANCOMBC_2.2.2.zip
macOS Binary (x86_64)	ANCOMBC_2.2.2.tgz
macOS Binary (arm64)	ANCOMBC_2.2.2.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