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metamicrobiomeR
View on CRAN: Click
here
Download and install metamicrobiomeR package within the R console
Install from CRAN:
install.packages("metamicrobiomeR")
Install from Github:
library("remotes")
install_github("cran/metamicrobiomeR")
Install by package version:
library("remotes")
install_version("metamicrobiomeR", "1.2")
Attach the package and use:
library("metamicrobiomeR")
Maintained by
Nhan Ho
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2019-09-03
Latest Update: 2020-11-09
Description:
Generalized Additive Model for Location, Scale and Shape (GAMLSS)
with zero inflated beta (BEZI) family for analysis of microbiome relative abundance data
(with various options for data transformation/normalization to address compositional effects) and
random effects meta-analysis models for meta-analysis pooling estimates across microbiome studies
are implemented.
Random Forest model to predict microbiome age based on relative abundances of
shared bacterial genera with the Bangladesh data (Subramanian et al 2014),
comparison of multiple diversity indexes using linear/linear mixed effect models
and some data display/visualization are also implemented.
The reference paper is published by
Ho NT, Li F, Wang S, Kuhn L (2019) .
How to cite:
Nhan Ho (2019). metamicrobiomeR: Microbiome Data Analysis & Meta-Analysis with GAMLSS-BEZI & Random Effects. R package version 1.2, https://cran.r-project.org/web/packages/metamicrobiomeR. Accessed 21 Nov. 2024.
Previous versions and publish date:
1.1 (2019-09-03 09:20)
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Other R packages that metamicrobiomeR depends,
imports, suggests or enhances
Complete documentation for metamicrobiomeR
Functions, R codes and Examples using
the metamicrobiomeR R package
Some associated functions: alpha.compare . alphadat . asum4 . covar.rm . gtab.3stud . kegg.12 . meta.niceplot . meta.taxa . metatab.show . microbiomeage . pathway.compare . read.multi . tabsex4 . taxa.compare . taxa.filter . taxa.mean.plot . taxa.meansdn . taxcomtab.show . taxtab6 .
Some associated R codes: alpha.compare.R . alphadat.R . asum4.R . covar.rm.R . globals.R . gtab.3stud.R . kegg.12.R . meta.niceplot.R . meta.taxa.R . metatab.show.R . microbiomeage.R . pathway.compare.R . read.multi.R . tabsex4.R . taxa.compare.R . taxa.filter.R . taxa.mean.plot.R . taxa.meansdn.R . taxcomtab.show.R . taxtab6.R . Full metamicrobiomeR package functions and examples
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