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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 (3.18)

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 "4.3") 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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ANCOMBC")
ANCOM Tutorial HTML R Script
ANCOM-BC Tutorial HTML R Script
ANCOM-BC2 Tutorial HTML R Script
SECOM Tutorial HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DifferentialExpression, Microbiome, Normalization, Sequencing, Software
Version 2.3.1
In Bioconductor since BioC 3.12 (R-4.0) (3 years)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports mia, stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils
Linking To
Suggests dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr
System Requirements
Enhances
URL https://github.com/FrederickHuangLin/ANCOMBC
Bug Reports https://github.com/FrederickHuangLin/ANCOMBC/issues
See More
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_2.3.1.tar.gz
Windows Binary ANCOMBC_2.3.1.zip (64-bit only)
macOS Binary (x86_64) ANCOMBC_2.3.1.tgz
macOS Binary (arm64) ANCOMBC_2.3.1.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