ANCOMBC

DOI: 10.18129/B9.bioc.ANCOMBC    

Analysis of compositions of microbiomes with bias correction

Bioconductor version: Release (3.15)

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 (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 were 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 "4.2") and enter:

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

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 ANCOMBC
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, Microbiome, Normalization, Sequencing, Software
Version 1.6.2
In Bioconductor since BioC 3.12 (R-4.0) (2 years)
License Artistic-2.0
Depends
Imports magrittr, Rdpack, rlang, microbiome, phyloseq, stats, DescTools, Hmisc, MASS, doParallel, doRNG, dplyr, energy, foreach, nlme, nloptr, parallel, tibble, tidyr
LinkingTo
Suggests knitr, rmarkdown, testthat, DT, corrplot, ggforce, limma, qwraps2 (>= 0.5.0), tidyverse
SystemRequirements
Enhances
URL https://github.com/FrederickHuangLin/ANCOMBC
BugReports https://github.com/FrederickHuangLin/ANCOMBC/issues
Depends On Me
Imports Me microbiomeMarker
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package ANCOMBC_1.6.2.tar.gz
Windows Binary ANCOMBC_1.6.2.zip
macOS 10.13 (High Sierra) ANCOMBC_1.6.2.tgz
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
Old Source Packages for BioC 3.15 Source Archive

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