# Network Construction and Comparison for Microbiome Data

## Documentation for package ‘NetCoMi’ version 1.1.0

- DESCRIPTION file.

## Help Pages

NetCoMi-package | NetCoMi: Network Comparison for Microbial Compositional Data
.boottest | Bootstrap Procedure for Testing Statistical Significance of Correlation Values
.calcAssociation | Compute associations between taxa
.calcProps | Calculate network properties
.getVecNames | Function for Generating Vector Names
.permTestDiffAsso | Permutation Tests for Determining Differential Associations
calcGCD | Graphlet Correlation Distance (GCD)
calcGCM | Graphlet Correlation Matrix (GCM)
cclasso | CCLasso: Correlation inference of Composition data through Lasso method
colToTransp | Adding transparency to a color
createAssoPerm | Create and store association matrices for permuted data
diffnet | Constructing Differential Networks for Microbiome Data
editLabels | Edit labels
gcoda | gCoda: conditional dependence network inference for compositional data
installNetCoMiPacks | Install all packages used within NetCoMi
multAdjust | Multiple testing adjustment
netAnalyze | Microbiome Network Analysis
netCompare | Group Comparison of Network Properties
netConstruct | Constructing Networks for Microbiome Data
plot | Plot Method for microNetProps Objects
plot.diffnet | Plot method for objects of class diffnet
plot.microNetProps | Plot Method for microNetProps Objects
plotHeat | Create a heatmap with p-values
print.GCD | Print method for GCD objects
print.summary.microNetComp | Summary Method for Objects of Class microNetComp
print.summary.microNetProps | Summary Method for Objects of Class microNetProps
renameTaxa | Rename taxa
summary.microNetComp | Summary Method for Objects of Class microNetComp
summary.microNetProps | Summary Method for Objects of Class microNetProps
testGCM | Test GCM(s) for statistical significance