ANCOMBC

DOI: 10.18129/B9.bioc.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 (3.17)

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>

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")

 

HTML R Script ANCOM
HTML R Script ANCOMBC
HTML R Script ANCOMBC2
HTML R Script SECOM
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, Microbiome, Normalization, Sequencing, Software
Version 2.1.1
In Bioconductor since BioC 3.12 (R-4.0) (2 years)
License Artistic-2.0
Depends R (>= 4.2.0)
Imports mia, stats, CVXR, DescTools, Hmisc, MASS, Rdpack, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, doParallel, doRNG, dplyr, emmeans, energy, foreach, lme4, lmerTest, magrittr, nloptr, parallel, rlang, rngtools, tibble, tidyr, utils
LinkingTo
Suggests knitr, rmarkdown, testthat, DT, caret, microbiome, tidyverse
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_2.1.1.tar.gz
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

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