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 (3.21)
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] (ORCID:
Maintainer: Huang Lin <huanglinfrederick at gmail.com>
citation("ANCOMBC")):
Installation
To install this package, start R (version "4.5") 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 |
| Tutorial on Data Sanity and Integrity Checks | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, Microbiome, Normalization, Sequencing, Software |
| Version | 2.9.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (4 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.3.0) |
| Imports | stats, CVXR, DescTools, Hmisc, MASS, Matrix, Rdpack, doParallel, doRNG, energy, foreach, gtools, lme4, lmerTest, multcomp, nloptr, parallel, utils |
| System Requirements | |
| URL | https://github.com/FrederickHuangLin/ANCOMBC |
| Bug Reports | https://github.com/FrederickHuangLin/ANCOMBC/issues |
See More
| Suggests | mia(>= 1.6.0), DT, S4Vectors, SingleCellExperiment, SummarizedExperiment, TreeSummarizedExperiment, dplyr, knitr, magrittr, microbiome, phyloseq, rmarkdown, testthat, tidyr, tidyverse |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | MiscMetabar |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ANCOMBC_2.9.0.tar.gz |
| Windows Binary (x86_64) | ANCOMBC_2.9.0.zip (64-bit only) |
| macOS Binary (x86_64) | ANCOMBC_2.9.0.tgz |
| 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ANCOMBC/ |
| Package Short Url | https://bioconductor.org/packages/ANCOMBC/ |
| Package Downloads Report | Download Stats |