microeco - Microbial Community Ecology Data Analysis

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.

Last updated 17 hours ago

9.98 score 216 stars 3 dependents 234 scripts 2.9k downloads

file2meco - Transform Files to 'microtable' Object with 'microeco' Package

Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.

Last updated 2 months ago

6.05 score 23 stars 75 scripts 1.2k downloads

meconetcomp - Compare Microbial Networks of 'trans_network' Class of 'microeco' Package

Compare microbial co-occurrence networks created from 'trans_network' class of 'microeco' package <https://github.com/ChiLiubio/microeco>. This package is the extension of 'trans_network' class of 'microeco' package and especially useful when different networks are constructed and analyzed simultaneously.

Last updated 15 days ago

4.42 score 8 stars 11 scripts 293 downloads

mecoturn - Decipher Microbial Turnover along a Gradient

Two pipelines are provided to study microbial turnover along a gradient, including the beta diversity and microbial abundance change. The 'betaturn' class consists of the steps of community dissimilarity matrix generation, matrix conversion, differential test and visualization. The workflow of 'taxaturn' class includes the taxonomic abundance calculation, abundance transformation, abundance change summary, statistical analysis and visualization. Multiple statistical approaches can contribute to the analysis of microbial turnover.

Last updated 4 months ago

3.48 score 3 stars 4 scripts 255 downloads