Unified methods for the inference and analysis of gene
regulatory networks
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Documentation for package ‘netZooR’ version 1.9.0
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. |