Package index • ramen

All functions

ConsortiumMetabolism(): Functional Microbiome Representation
ConsortiumMetabolismAlignment(): Constructor for ConsortiumMetabolismAlignment Objects
ConsortiumMetabolismSet(): Set of ConsortiumMetabolism Objects
align(): Align Consortium Metabolisms
compareAlignments(): Compare Alignments (Deprecated)
consensusPathways(): Get Consensus Pathways
consortia(): Get the Consortia
description() `description<-`(): Get or Set Object Description
extractCluster(): Extract a Cluster
functionalGroups(): Get Functional Groups
importMisosoup(): Import and Process Misosoup Data
metabolites(): Get Metabolites
misosoup24: Example Data from MiSoSoup 2024
name() `name<-`(): Get or Set Object Name
overviewMisosoup(): Overview of Misosoup Data Structure
pathways(): Retrieve Metabolic Pathways
pivotCM(): Pivot ConsortiaMetabolism Input Data
plot(<ConsortiumMetabolism>,<ANY>): Plot a ConsortiumMetabolism object
plot(<ConsortiumMetabolismAlignment>,<ANY>): Plot a ConsortiumMetabolismAlignment object
plot(<ConsortiumMetabolismSet>,<ANY>): Plot a ConsortiumMetabolismSet object
plotAlignmentHeatmap(): Plot Alignment Heatmap (Deprecated)
plotAlignmentNetwork(): Plot Alignment Network (Deprecated)
plotDirectedFlow(): Plot a Directed Graph Emphasizing Flow
prevalence(): Get Pathway Prevalence
scores(): Get Alignment Scores
sharedPathways(): Get Shared Pathways
show(<ConsortiumMetabolism>): Show Method for ConsortiumMetabolism Object
show(<ConsortiumMetabolismAlignment>): Show method for ConsortiumMetabolismAlignment Objects
show(<ConsortiumMetabolismSet>): Show Method for ConsortiumMetabolismSet Object
similarityMatrix(): Get Similarity Matrix
species(): Return Species in a Consortium
synCM(): Generate Synthetic Consortium Metabolism
uniquePathways(): Get Unique Pathways