# Unified methods for the inference and analysis of gene regulatory networks

## Documentation for package ‘netZooR’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

adjMatToElist | converts adjacency matrix to edge list
alpaca | Main ALPACA function
alpacaCommunityStructureRotation | Comparing node community membership between two networks
alpacaComputeDifferentialScoreFromDWBM | Compute Differential modularity score from differential modularity matrix
alpacaComputeDWBMmatmScale | Differential modularity matrix
alpacaComputeWBMmat | Compute modularity matrix for weighted bipartite network
alpacaCrane | Find the robust nodes in ALPACA community using CRANE
alpacaDeltaZAnalysis | Edge subtraction method (CONDOR optimizaton)
alpacaDeltaZAnalysisLouvain | Edge subtraction method (Louvain optimizaton)
alpacaExtractTopGenes | Extract core target genes in differential modules
alpacaGenLouvain | Generalized Louvain optimization
alpacaGetMember | get the member vector from alpaca object
alpacaGOtabtogenes | The top GO term associated genes in each module
alpacaGoToGenes | Map GO terms to gene symbols
alpacaListToGo | GO term enrichment for a list of gene sets
alpacaMetaNetwork | Create alpacaMetaNetwork for Louvain optimization
alpacaNodeToGene | Remove tags from gene names
alpacaObjectToDfList | Converts alpaca output into list of data frames
alpacaRotationAnalysis | Community comparison method (CONDOR optimizaton)
alpacaRotationAnalysisLouvain | Community comparison method (CONDOR optimizaton)
alpacaSimulateNetwork | Simulated networks
alpacaTestNodeRank | Enrichment in ranked list
alpacaTidyConfig | Renumbering community membership vector
alpacaTopEnsembltoTopSym | Translating gene identifiers to gene symbols
alpacaWBMlouvain | Generalized Louvain method for bipartite networks
condorCluster | Main clustering function for condor.
condorCoreEnrich | Compare qscore distribution of a subset of nodes to all other nodes.
condorCreateObject | creates condor object
condorMatrixModularity | Iteratively maximize bipartite modularity.
condorModularityMax | Iteratively maximize bipartite modularity.
condorPlotCommunities | Plot adjacency matrix with links grouped and colored by community
condorPlotHeatmap | Plot weighted adjacency matrix with links grouped by community
condorQscore | Calculate Qscore for all nodes
condorRun | Run CONDOR clustering
craneBipartite | Pertrubs the bipartite network with fixed node strength
craneUnipartite | Pertrubs the unipartite network with fixed node strength from adjacency matrix
createCondorObject | Create list amenable to analysis using 'condor' package.
createPandaStyle | Create a Cytoscape visual style for PANDA network
degreeAdjust | Function to adjust the degree so that the hub nodes are not penalized in z-score transformation
dragon | Run DRAGON in R.
elistAddTags | Adds "_A" to first column and "_B" to second column
elistIsEdgeOrderEqual | check if first two columns are identical
elistRemoveTags | undo elistAddTags
elistSort | Sorts the edge list based on first two columns in alphabetical order
elistToAdjMat | Converts edge list to adjacency matrix
exon.size | Gene length
genes | Example of a gene list
isElist | Check if data frame is an edge list
jutterDegree | CRANE Beta perturbation function. This function will add noice to the node strength sequence.
lioness | Compute LIONESS (Linear Interpolation to Obtain Network Estimates for Single Samples)
lionessPy | Run python implementation of LIONESS
monster | MOdeling Network State Transitions from Expression and Regulatory data (MONSTER)
monsterBereFull | Bipartite Edge Reconstruction from Expression data (composite method with direct/indirect)
monsterCalculateTmPValues | Calculate p-values for a tranformation matrix
monsterCheckDataType | Checks that data is something MONSTER can handle
monsterdTFIPlot | This function plots the Off diagonal mass of an observed Transition Matrix compared to a set of null TMs
monsterGetTm | monsterGetTm
monsterHclHeatmapPlot | Transformation matrix plot
monsterMonsterNI | Bipartite Edge Reconstruction from Expression data
monsterPlotMonsterAnalysis | monsterPlotMonsterAnalysis
monsterPrintMonsterAnalysis | monsterPrintMonsterAnalysis
monsterRes | MONSTER results from example cell-cycle yeast transition
monsterTransformationMatrix | Bi-partite network analysis tools
monsterTransitionNetworkPlot | This function uses igraph to plot the transition matrix (directed graph) as a network. The edges in the network should be read as A 'positively/negatively contributes to' the targeting of B in the target state.
monsterTransitionPCAPlot | Principal Components plot of transformation matrix
mut.ucec | Example of mutation data
otter | Run OTTER in R
pandaDiffEdges | Identify differential edges in two PANDA networks
pandaPy | Run Python implementation PANDA in R
pandaToAlpaca | Use two PANDA network to generate an ALPACA result
pandaToCondorObject | Turn PANDA network into a CONDOR object
runEgret | Run EGRET in R
sambar | Main SAMBAR function.
sambarConvertgmt | Convert .gmt files into a binary matrix.
sambarCorgenelength | Normalize gene mutation scores by gene length.
sambarDesparsify | De-sparsify gene-level mutation scores into gene set-level mutation scores.
small1976 | Pollinator-plant interactions
sourcePPI | Source the Protein-Protein interaction in STRING database
spider | Seeding PANDA Interactions to Derive Epigenetic Regulation
visPandaInCytoscape | Plot PANDA network in Cytoscape
yeast | Toy data derived from three gene expression datasets and a mapping from transcription factors to genes.