ANCOMBC

This is the development version of ANCOMBC; for the stable release version, see ANCOMBC.

Microbiome differential abudance and correlation analyses with bias correction

Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("ANCOMBC")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, Microbiome, Normalization, Sequencing, Software
Version	2.5.0
In Bioconductor since	BioC 3.12 (R-4.0) (3.5 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
System Requirements
URL	https://github.com/FrederickHuangLin/ANCOMBC
Bug Reports	https://github.com/FrederickHuangLin/ANCOMBC/issues

Suggests	dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr
Linking To
Enhances
Depends On Me
Imports Me	benchdamic, microbiomeMarker
Suggests Me	dar
Links To Me
Build Report	Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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