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microeco (version 0.7.1)

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 statistics, beta diversity statistics, differential abundance test, environmental data analysis, null model analysis, network analysis, machine learning and functional analysis.

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Install

install.packages('microeco')

Monthly Downloads

2,977

Version

0.7.1

License

GPL-3

Issues

85

Pull Requests

0

Stars

228

Forks

67

Maintainer

Chi Liu

Last Published

March 19th, 2022

Functions in microeco (0.7.1)

dropallfactors

Remove all factors in a data frame
clone

Copy an R6 class object completely
Tax4Fun2_KEGG

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

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

The dataset in the microeco package
otu_table_ITS

The OTU table of the ITS dataset in the microeco package
otu_table_16S

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

The FUNGuild database for fungi trait identification in the microeco package
phylo_tree_16S

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

The sample information of ITS dataset in the microeco package
tidy_taxonomy

Clear up the taxonomic table to make taxonomic assignments consistent.
prok_func_FAPROTAX

The modified FAPROTAX trait database in the microeco package
prok_func_NJC19_list

The modified NJC19 database in the microeco package
taxonomy_table_ITS

The taxonomic information of ITS dataset in the microeco package
trans_abund

Create trans_abund object to transform taxonomic abundance for plotting.
fungi_func_FungalTraits

The FungalTraits database for fungi trait identification in the microeco package
sample_info_16S

The sample information of 16S dataset in the microeco package
rep_fasta_16S

The fasta file of 16S dataset used in tax4fun2 method.
trans_func

Create trans_func object for functional analysis.
trans_network

Create trans_network object for co-occurrence network analysis.
trans_nullmodel

Create trans_nullmodel object.
taxonomy_table_16S

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

Create trans_beta object for the analysis of distance matrix of beta-diversity.
trans_alpha

Create trans_alpha object for alpha diveristy statistics and plotting.
trans_classifier

Create trans_classifier object for machine-learning-based model prediction.
trans_venn

Create trans_venn object.
trans_env

Create trans_env object for the analysis of the effects of environmental factors on communities.
trans_diff

Create trans_diff object for the differential analysis on the taxonomic abundance.
color_palette_20

A color palette for 20 elements.
env_data_16S

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