Microbial Community Ecology Data Analysis
Copy an R6 class object
Remove all factors in a data frame
Introduction to microeco package ([https://github.com/ChiLiubio/microe...
Create microtable
object to store and manage all the basic files.
Clean up the taxonomic table to make taxonomic assignments consistent.
Create trans_abund
object for taxonomic abundance visualization.
Create trans_alpha
object for alpha diversity statistics and visuali...
Create trans_beta
object for beta-diversity analysis
Create trans_classifier
object for machine-learning-based model pred...
Create trans_diff
object for the differential analysis on the taxono...
Create trans_env
object to analyze the association between environme...
Create trans_func
object for functional prediction.
Create trans_network
object for network analysis.
Feature abundance normalization/transformation.
Create trans_nullmodel
object for phylogeny- and taxonomy-based null...
Create trans_venn
object for the Venn diagram, petal plot and UpSet ...
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.