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microeco (version 0.16.0)

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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Version

Install

install.packages('microeco')

Monthly Downloads

2,977

Version

0.16.0

License

GPL-3

Issues

88

Pull Requests

0

Stars

230

Forks

67

Maintainer

Chi Liu

Last Published

April 14th, 2023

Functions in microeco (0.16.0)

microeco

Introduction to microeco package
dropallfactors

Remove all factors in a data frame
clone

Copy an R6 class object completely
microtable

Create microtable object to store and manage all the basic files.
Tax4Fun2_KEGG

The KEGG data files used in the cal_tax4fun2 function of trans_func class.
env_data_16S

The environmental factors for the 16S dataset in the microeco package
fungi_func_FungalTraits

The FungalTraits database for fungi trait identification in the microeco package
color_palette_20

A color palette for 20 elements.
fungi_func_FUNGuild

The FUNGuild database for fungi trait identification in the microeco package
dataset

The dataset in the microeco package
otu_table_ITS

The OTU table of the ITS dataset in the microeco package
taxonomy_table_16S

The taxonomic information of 16S dataset in the microeco package
sample_info_ITS

The sample information of ITS dataset in the microeco package
otu_table_16S

The OTU table of the 16S dataset in the microeco package
prok_func_NJC19_list

The modified NJC19 database in the microeco package
prok_func_FAPROTAX

The modified FAPROTAX trait database in the microeco package
phylo_tree_16S

The phylogenetic tree of 16S dataset in the microeco package
sample_info_16S

The sample information of 16S dataset in the microeco package
tidy_taxonomy

Clean up the taxonomic table to make taxonomic assignments consistent.
taxonomy_table_ITS

The taxonomic information of ITS dataset in the microeco package