Microbial Community Ecology Data Analysis

[Up] [Top]

Documentation for package ‘microeco’ version 1.6.0

Help Pages

clone Copy an R6 class object
dataset The dataset structured with microtable class for the demonstration of examples
dropallfactors Remove all factors in a data frame
env_data_16S The environmental factors for the 16S example data
fungi_func_FungalTraits The FungalTraits database for fungi trait prediction
fungi_func_FUNGuild The FUNGuild database for fungi trait prediction
microeco Introduction to microeco package (https://github.com/ChiLiubio/microeco)
microtable Create 'microtable' object to store and manage all the basic files.
otu_table_16S The OTU table of the 16S example data
otu_table_ITS The OTU table of the ITS example data
phylo_tree_16S The phylogenetic tree of 16S example data
prok_func_FAPROTAX The modified FAPROTAX trait database
prok_func_NJC19_list The modified NJC19 database
sample_info_16S The sample information of 16S example data
sample_info_ITS The sample information of ITS example data
Tax4Fun2_KEGG The KEGG data files used in the trans_func class
taxonomy_table_16S The taxonomic information of 16S example data
taxonomy_table_ITS The taxonomic information of ITS example data
tidy_taxonomy Clean up the taxonomic table to make taxonomic assignments consistent.
trans_abund Create 'trans_abund' object for plotting taxonomic abundance.
trans_alpha Create 'trans_alpha' object for alpha diversity statistics and plot.
trans_beta Create 'trans_beta' object for beta-diversity analysis based on the distance matrix
trans_classifier Create trans_classifier object for machine-learning-based model prediction.
trans_diff Create 'trans_diff' object for the differential analysis on the taxonomic abundance
trans_env Create 'trans_env' object to analyze the association between environmental factor and microbial community.
trans_func Create 'trans_func' object for functional prediction.
trans_network Create 'trans_network' object for network analysis.
trans_norm Feature abundance normalization/transformation.
trans_nullmodel Create 'trans_nullmodel' object for phylogeny- and taxonomy-based null model analysis.
trans_venn Create 'trans_venn' object for the Venn diagram, petal plot and UpSet plot.