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microeco (version 0.3.1)

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 and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis.

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Version

Install

install.packages('microeco')

Monthly Downloads

2,977

Version

0.3.1

License

GPL-3

Maintainer

Chi Liu

Last Published

November 24th, 2020

Functions in microeco (0.3.1)

clone

Copy an R6 class object completely
otu_table_16S

The OTU table of the 16S dataset in the microeco package
meco2phyloseq

Transform microtable object in microeco package to the phyloseq object in phyloseq package.
microtable

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

Remove all factors in a data frame
fungi_func

The fungi function database in the microeco package
env_data_16S

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

The dataset in the microeco package
ko_map

The KEGG pathway annotation database in the microeco package
otu_table_ITS

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

The prokaryotic function database in the microeco package
sample_info_16S

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

Create trans_alpha object for alpha diveristy statistics and plotting.
trans_abund

Create trans_abund object to transform taxonomic abundance for plotting.
taxonomy_table_ITS

The taxonomic information of ITS dataset in the microeco package
tidy_taxonomy

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

Create trans_nullmodel object.
trans_network

Create trans_network object for co-occurrence network analysis.
trans_venn

Create trans_venn object.
phyloseq2meco

Transform the phyloseq object in phyloseq package to microtable object in microeco package.
trans_func

Create trans_func object for functional analysis.
trans_beta

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

Create trans_env object for the analysis of the effects of environmental factors on communities.
phylo_tree_16S

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

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