DOI: 10.18129/B9.bioc.ANCOMBC  

Microbiome differential abudance and correlation analyses with bias correction

Bioconductor version: Release (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>

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


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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


biocViews DifferentialExpression, Microbiome, Normalization, Sequencing, Software
Version 2.4.0
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
Suggests dplyr, knitr, rmarkdown, testthat, DT, tidyr, tidyverse, microbiome, magrittr
Depends On Me
Imports Me benchdamic, microbiomeMarker
Suggests Me
Links To Me
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