MetaDICT

This is the released version of MetaDICT; for the devel version, see MetaDICT.

Microbiome data integration method via shared dictionary learning

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DOI: 10.18129/B9.bioc.MetaDICT

Bioconductor version: Release (3.22)

MetaDICT is a method for the integration of microbiome data. This method is designed to remove batch effects and preserve biological variation while integrating heterogeneous datasets. MetaDICT can better avoid overcorrection when unobserved confounding variables are present.

Author: Bo Yuan [aut, cre] ORCID iD ORCID: 0009-0008-5428-4447 , Shulei Wang [aut]

Maintainer: Bo Yuan <boyuan5 at illinois.edu>

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

Installation

To install this package, start R (version "4.5") and enter:


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

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("MetaDICT")

MetaDICT Tutorial HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews BatchEffect, Clustering, Microbiome, Sequencing, Software

Version 1.0.0

In Bioconductor since BioC 3.22 (R-4.5) (< 6 months)

License Artistic-2.0

Depends R (>= 4.2.0)

Imports stats, RANN, igraph, vegan, edgeR, ecodist, ggplot2, viridis, ggpubr, ape, cluster, matrixStats

System Requirements

URL https://github.com/BoYuan07/MetaDICT

Bug Reports https://github.com/BoYuan07/MetaDICT/issues

Suggests BiocStyle, knitr, rmarkdown, DT, ggraph, tidyverse, testthat (>= 3.0.0)

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Package Archives

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

Source Package MetaDICT_1.0.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) MetaDICT_1.0.0.tgz

macOS Binary (arm64) MetaDICT_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/MetaDICT

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MetaDICT

Bioc Package Browser https://code.bioconductor.org/browse/MetaDICT/

Package Short Url https://bioconductor.org/packages/MetaDICT/

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