/ANCOMBC

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

Primary LanguageR

ANCOMBC

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, manuscript in preparation), 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.

To install the latest release version of ANCOMBC

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("ANCOMBC")

Usage

library(ANCOMBC)
?ancombc2
?ancombc 
?ancom
?secom_linear
?secom_dist

Author: Huang Lin

Maintainer: Huang Lin: huanglinfrederick@gmail.com