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microeco (version 2.3.0)

Microbial Community Ecology Data Analysis

Description

A series of data analysis approaches for microbiome data based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.

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Install

install.packages('microeco')

Monthly Downloads

2,141

Version

2.3.0

License

GPL-3

Issues

39

Pull Requests

0

Stars

292

Forks

80

Maintainer

Chi Liu

Last Published

July 7th, 2026

Functions in microeco (2.3.0)

clone

Copy an R6 class object
microeco

Introduction to microeco package (https://github.com/ChiLiubio/microeco)
dropallfactors

Remove all factors in a data frame
microtable

Create microtable object to store and manage all the basic data.
phylo_tree_16S

The phylogenetic tree of 16S example data
prok_func_NJC19_list

The NJC19 database
dataset

The dataset structured with microtable class for the demonstration of examples
otu_table_ITS

The OTU table of the ITS example data
env_data_16S

The environmental factors for the 16S example data
Tax4Fun2_KEGG

The KEGG data files used in the trans_func class
otu_table_16S

The OTU table of the 16S example data
taxonomy_table_ITS

The taxonomic information of ITS example data
soil_microb

Microtable object of prokaryotic sequencing data from soil and maize in an agricultural field experiment with crop rotation and fertilization treatments (DOI: 10.1007/s11104-024-06847-9).
taxonomy_table_16S

The taxonomic information of 16S example data
fungi_func_FUNGuild

The FUNGuild database for fungi trait prediction
fungi_func_FungalTraits

The FungalTraits database for fungi trait prediction
sample_info_ITS

The sample information of ITS example data
soil_metab

Microtable object of non-targeted metabolome data from bulk soil and maize rhizosphere soil in an agricultural field experiment with crop rotation and fertilization treatments (DOI: 10.1007/s11104-024-06847-9).
sample_info_16S

The sample information of 16S example data
prok_func_FAPROTAX

Customized FAPROTAX trait database