Package index

Main functions

netConstruct()

Constructing Networks for Microbiome Data

netAnalyze()

Microbiome Network Analysis

netCompare()

Group Comparison of Network Properties

diffnet()

Constructing Differential Networks for Microbiome Data

installNetCoMiPacks()

Install all packages used within NetCoMi

Association estimation

cclasso()

CCLasso: Correlation inference of Composition data through Lasso method

gcoda()

gCoda: conditional dependence network inference for compositional data

Helpers

createAssoPerm()

Create and store association matrices for permuted data

colToTransp()

Adding transparency to a color

calcGCD()

Graphlet Correlation Distance (GCD)

calcGCM()

Graphlet Correlation Matrix (GCM)

editLabels()

Edit labels

multAdjust()

Multiple testing adjustment

plotHeat()

Create a heatmap with p-values

renameTaxa()

Rename taxa

testGCM()

Test GCM(s) for statistical significance

S3 methods

plot(<diffnet>)

Plot method for objects of class diffnet

plot(<microNetProps>)

Plot Method for microNetProps Objects

print(<GCD>)

Print method for GCD objects

summary(<microNetComp>) print(<summary.microNetComp>)

Summary Method for Objects of Class microNetComp

summary(<microNetProps>) print(<summary.microNetProps>)

Summary Method for Objects of Class microNetProps