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microeco - Microbial Community Ecology Data Analysis

A series of data analysis approaches for microbiome data 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.

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10.36 score 281 stars 3 dependents 420 scripts 3.3k 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.

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6.16 score 28 stars 144 scripts 1.4k 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.

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4.72 score 12 stars 22 scripts 364 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.

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3.95 score 3 stars 6 scripts 330 downloads