Man pages for netZoo/netZooR
Unified methods for the inference and analysis of gene regulatory networks
| adj2el | Convert a bipartite adjacency matrix to an edgelist |
| adj2regulon | Convert bipartite adjacency to regulon |
| 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... |
| 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 |
| annotateFromBiomart | Annotate your Expression Set with biomaRt |
| bladder | Bladder RNA-seq data from the GTEx consortium |
| BuildSubnetwork | Find the subnetwork of significant edges connecting the... |
| CalculatePValues | Calculate p-values for all edges in the network using a... |
| checkMisAnnotation | Check for wrong annotation of a sample using classical MDS... |
| checkTissuesToMerge | Check tissues to merge based on gene expression profile |
| cobra | Run COBRA in R |
| condorCluster | Main clustering function for condor. |
| condorCoreEnrich | Compare qscore distribution of a subset of nodes to all other... |
| condorCreateObject | creates condor object |
| condorMatrixModularity | Iteratively maximize bipartite modularity. |
| condorModularityMax | Iteratively maximize bipartite modularity. |
| condorPlotCommunities | Plot adjacency matrix with links grouped and colored by... |
| condorPlotHeatmap | Plot weighted adjacency matrix with links grouped by... |
| 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... |
| 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... |
| domonster | MONSTER quick-start with pre-made regulatory networks |
| downloadGTEx | Download GTEx files and turn them into ExpressionSet object |
| dragon | Run DRAGON in R. |
| el2adj | Convert bipartite edge list to adjacency mat |
| el2regulon | Convert a bipartite edgelist to regulon |
| 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... |
| elistToAdjMat | Converts edge list to adjacency matrix |
| exon.size | Gene length |
| extractMatrix | Extract the appropriate matrix |
| filterGenes | Filter specific genes |
| filterLowGenes | Filter genes that have less than a minimum threshold CPM for... |
| filterMissingGenes | Filter genes not expressed in any sample |
| filterSamples | Filter samples |
| FindConnectionsForAllHopCounts | For all hop counts up to the maximum, find subnetworks... |
| FindSignificantEdgesForHop | Find the subnetwork of significant edges n / 2 hops away from... |
| GenerateNullPANDADistribution | Generate a null distribution of edge scores for PANDA-like... |
| genes | Example of a gene list |
| isElist | Check if data frame is an edge list |
| jutterDegree | CRANE Beta perturbation function. This function will add... |
| lioness | Compute LIONESS (Linear Interpolation to Obtain Network... |
| lionessPy | Run python implementation of LIONESS |
| monster | MOdeling Network State Transitions from Expression and... |
| monsterBereFull | Bipartite Edge Reconstruction from Expression data (composite... |
| 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... |
| 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... |
| monsterTransitionPCAPlot | Principal Components plot of transformation matrix |
| mut.ucec | Example of mutation data |
| normalizeTissueAware | Normalize in a tissue aware context |
| 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 |
| plotCMDS | Plot classical MDS of dataset |
| plotDensity | Density plots of columns in a matrix |
| plotHeatmap | Plot heatmap of most variable genes |
| PlotNetwork | Plot the networks, using different colors for transcription... |
| priorPp | Filter low confident edge signs in the prior network using... |
| puma | PANDA using microRNA associations |
| qsmooth | Quantile shrinkage normalization |
| qstats | Compute quantile statistics |
| RunBLOBFISH | Given a set of genes of interest, full bipartite networks... |
| 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... |
| SignificantBreadthFirstSearch | Find all significant edges adjacent to the starting nodes,... |
| skin | Skin RNA-seq data from the GTEx consortium |
| small1976 | Pollinator-plant interactions |
| sourcePPI | Source the Protein-Protein interaction in STRING database |
| spider | Seeding PANDA Interactions to Derive Epigenetic Regulation |
| tiger | TIGER main function |
| TIGER_expr | TIGER example expression matrix |
| TIGER_prior | TIGER example prior network |
| visPandaInCytoscape | Plot PANDA network in Cytoscape |
| yeast | Toy data derived from three gene expression datasets and a... |
