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microeco (version 1.14.0)

Microbial Community Ecology Data Analysis

Description

A series of statistical and plotting approaches in microbial community ecology 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

2,977

Version

1.14.0

License

GPL-3

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Repository

https://github.com/ChiLiubio/microeco

Maintainer

Chi Liu

Last Published

March 28th, 2025

Functions in microeco (1.14.0)

sample_info_16S

The sample information of 16S example data

Clean up the taxonomic table to make taxonomic assignments consistent.

sample_info_ITS

The sample information of ITS example data

Create trans_abund object for taxonomic abundance visualization.

taxonomy_table_ITS

The taxonomic information of ITS example data

The OTU table of the ITS example data

taxonomy_table_16S

The taxonomic information of 16S example data

The phylogenetic tree of 16S example data

prok_func_FAPROTAX

The modified FAPROTAX trait database

prok_func_NJC19_list

The modified NJC19 database

The KEGG data files used in the trans_func class

Copy an R6 class object

Remove all factors in a data frame

fungi_func_FUNGuild

The FUNGuild database for fungi trait prediction

The dataset structured with microtable class for the demonstration of examples

Create microtable object to store and manage all the basic files.

The environmental factors for the 16S example data

fungi_func_FungalTraits

The FungalTraits database for fungi trait prediction

The OTU table of the 16S example data

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