Package index
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MicrobiomeFunction() - Functional Microbiome Representation based on
TreeSummarizedExperiment
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MicrobiomeFunctionAlignment() - Alignment of
MicrobiomeFunctionobjects
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MicrobiomeFunctionSet() - Set of
MicrobiomeFunctionObjects
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compareAlignments() - Compare Alignments
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.multipleAlignment() - Multiple Alignment of
MicrobiomeFunctionObjects
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.rxnsPerLevel() - Get Count of Reactions Per Level of Alignment
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.scoreAlignment() - Scoring Algorithm for MiCoAl Objects
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findEdges() - Get All Edges of a Community
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getCo() - Get the Community
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getEdges() - Get Edges From a
MicrobiomeFunctionObject
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getMet() - Get Metabolites
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getSpecies() - Return Species in a Microbiome
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makeSynMiCo() - Generate Random Synthetic Microbial Communities
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misosoup24 - Example Data from MiSoSoup 2024
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pivotMF() - Functions to Change the orientation of MiCo Input Data
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plotAlignmentHeatmap() - MiCoAl Heatmap
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plotAlignmentNetwork() - MiCoAl Network Plot
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show(<MicrobiomeFunction>) - Show Method for
MicrobiomeFunctionObject
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show(<MicrobiomeFunctionAlignment>) - Show method for
MicrobiomeFunctionAlignmentObjects