Package index • ramen

All functions

ConsortiumMetabolism(): Functional Microbiome Representation based on TreeSummarizedExperiment

ConsortiumMetabolismSet(): Set of ConsortiumMetabolism Objects

align(): Align a ConsortiaMetabolismSet Object

cluster(): Cluster a ConsortiaMetabolismSet Object

compareAlignments(): Compare Alignments

compareSpecies(): Compare Species

.rxnsPerLevel(): Get Count of Reactions Per Level of Alignment

getCluster(): Get a cluster from a ConsortiaMetabolismSet Object

getCo(): Get the Consortia

getEdges(): Get Edges From a ConsortiumMetabolism Object

getFunctionalGroups(): Get Functional Groups

getMet(): Get Metabolites

getSpecies(): Return Species in a Consortium

importMisosoup(): Import and Process Misosoup Data

misosoup24: Example Data from MiSoSoup 2024

modify(): Modify a ConsortiaMetabolismSet Object

overviewMisosoup(): Overview of Misosoup Data Structure

pivotCM(): Pivot ConsortiaMetabolism Input Data

plotAlignmentHeatmap(): MiCoAl Heatmap

plotAlignmentNetwork(): MiCoAl Network Plot

plotDirectedFlow(): Plot a Directed Graph Emphasizing Flow

setDesc(): Set Names or description of ramen Objects

setName(): Set Names or description of ramen Objects

show(<ConsortiumMetabolism>): Show Method for ConsortiumMetabolism Object

show(<ConsortiumMetabolismAlignment>): Show method for ConsortiumMetabolismAlignment Objects

show(<ConsortiumMetabolismSet>): Show Method for ConsortiumMetabolismSet Object

synCM(): Generate Random Synthetic Consortium Metabolism