Man pages for xia-lab/miRNetR
A companion R package for the miRNet web server
| all.numeric | Check/Convert Values to Numeric |
| AutoNorm | Auto Normalization |
| CalculateMirTargetSet | Calculate miRNA Target Set |
| CalculatePairwiseDiff | Calculate Pairwise Difference |
| checkMiRNAVersion | Check miRNA Version |
| CleanMemory | Clean Memory |
| ClearFactorStrings | Clear Factor Strings |
| ClearStrings | Clear String |
| ComputeColorGradient | Compute Color Gradient |
| ComputePCSFNet | Compute Network based on Prize-collecting Steiner Forest... |
| ComputeSubnetStats | Compute Subnetwork Stats |
| convertIgraph2JSON | Convert Igraph to JSON |
| convertIgraph2JSONFromFile | Convert Igraph to JSON |
| CreateMirNets | Create miRNA Network |
| DecomposeMirGraph | Decompose to Subnetworks |
| doAnnotation | Annotate |
| doEntrez2SymbolMapping | Entrez ID to Gene Symbol |
| doGeneIDMapping | Gene ID Mapping |
| doMirGeneAnnotation | Gene Annotation |
| doProbeMapping | Probe Mapping |
| doSymbol2EntrezMapping | Gene Symbol to Entrez ID |
| ExcludeNodes | Exlude Nodes |
| ExtractMirNetModule | Extract miRNA Network Module |
| FilterMirNet | Filter miRNA Network |
| FilterMirNetByList | Filter miRNA Network by List |
| FindCommunities | Find Communities |
| generate_breaks | Generate Breaks |
| GetAnotNames | Get annotated names |
| GetBashFullPath | Get Bash Full Path |
| GetClassInfo | Get class info |
| GetColorGradient | Get Color Gradient |
| GetColorSchema | Get Color Schema |
| getExpColors | Colors Based on Expression |
| GetExtendRange | Get Extend Range |
| GetFC | Get Fold Change |
| GetMinConnectedGraphs | Get Minimally Connected Graphs |
| GetMirResCol | Get Result Column |
| GetMirResRowNames | Get Result Row |
| GetNetNames | Get Network Names |
| GetNetNms | Network Names |
| GetNetsNameString | Get Network Names as String |
| GetNetStatByType | Get Network Stats by Type |
| GetNetStatColNames | Network Stats Column Names |
| GetNetStatMatrix | Get Network Stats as Matrix |
| GetNetStats | Get Network Stats |
| GetNetworkTopology | Get Network Topology |
| GetQueryNum | Number of Queries |
| GetRandomMirTargetGenes | Get Random miRNA Target Genes |
| GetRandomXenoMirTargetGenes | Get Random Xeno-miRNA Target Genes |
| GetRCommandHistory | Export R Command History |
| GetSeedsColumn | Get Seeds Column |
| GetSeq | Get miRNA Accession |
| GetSeqnm | Get miRNA Name |
| GetShortestPaths | Get Shortest Paths |
| GetSigGenes | Get significant genes |
| GetTableNames | Get Table Names |
| GetTtestP | Get p-value from t-test |
| GetTypeNum | Number of Types |
| GetUniqueClassNames | Get Unique Class Names |
| GetUniqueDiseaseNames | Get Unique Disease Names |
| GetUniqueEntries | Get Unique Entries |
| GetUniqueEpigeneNames | Get Unique Epigene Names |
| GetUniqueMoleculeNames | Get Unique Molecule Names |
| GetUniqueSourceNames | Get Unique Source Names |
| GetUniqueSpeciesNames | Get Unique Species Names |
| GetUnmappedNum | Number of Unmapped |
| GetUpdateClassNames | Get Updated Class Names |
| GetUpdateSpeNames | Get Updated Species Names |
| gg_color_hue | Group Color Palette |
| hex2rgba | Hex color to RGBA format |
| Init.Data | Initiate Data |
| layout_in_circles | Layout in Circles |
| LoadClusterLib | Load Cluster Annotation Library |
| LoadDiseaseLib | Load Disease Library |
| LoadFuncLib | Load miRNA Functional Annotation Library |
| LoadGOLib | Load Gene Ontology Library |
| LoadHMDDLib | Load HMDD Library |
| LoadKEGGLib | Load KEGG Library |
| LoadmiRFamLib | Load miRNA Family Library |
| LoadREACTOMELib | Load Reactome Library |
| LoadTFLib | Load Transcription Factor Library |
| LoadTissueLib | Load Tissue Library |
| LogNorm | Log Normalization |
| miRNA_PrecursorToMature | miRNA Name Conversion From Precursor to Mature |
| myave | Average |
| PerformAPIMirTargetEnrichAnalysis | Perform miRNA Target Enrichment Analysis (API) |
| PerformArrayDataNormalization | Peform array data normalization |
| PerformCircRNAMapping | Perform Circular RNA Mapping |
| PerformCountDataNormalization | Perform count data normalization #' @export |
| PerformDataAnnot | Peform data annotation |
| PerformDisMapping | Perform Disease Mapping |
| PerformEdgeR | Perform EdgeR |
| PerformGeneAnnotation | Perform Gene Annotation |
| PerformHTqPCR | Perform HTqPCR |
| PerformLayOut | Apply Graph Layout |
| PerformLimma | Perform limma |
| PerformLncRNAMapping | Perform Long Noncoding RNA Mapping |
| PerformMir2EpiMapping | Perform Epigene Mapping |
| PerformMirGeneMapping | Perform miRNA Gene Mapping |
| PerformMirTargetEnrichAnalysis | Perform miRNA Target Enrichment Analysis |
| PerformMolMapping | Perform Molecule Mapping |
| PerformPseudoMapping | Perform Pseudogene Mapping |
| PerformQpcrDataNormalization | Perform qPCR data normalization |
| PerformSncRNAMapping | Perform Small Untranslated RNA Mapping |
| PerformSNPMirGeneMapping | Perform SNP Mapping |
| PerformSpeciesMapping | Species Mapping |
| PerformTFMapping | Perform Transcription Factor Mapping |
| PerformXenoMirGeneMapping | Xeno-miRNA Gene Target Mapping |
| PlotBetweennessHistogram | Plot Betweenness Histogram |
| PlotDataOverview | Plot Data Overview |
| PlotDegreeHistogram | Plot Degree Histogram |
| PrepareCSV | Prepare CSV |
| PrepareGraphML | Prepare Graph ML |
| PrepareJsonFromR | Prepare JSON File |
| PrepareMirNet | Prepare miRNA Network |
| queryGeneDB | Query Gene DB |
| Query.miRNetDB | Query miRNet DB |
| QueryMultiList | Query Multi List |
| QueryMultiListMir | Query Multi List miRNA |
| QueryPpiSQLiteZero | Query Protein-Protein Interaction |
| QueryTFSQLite | Query Transcription Factor |
| QueryXenoMirSQLite | Query Xeno-miRNA |
| ReadGraphData | Read Graph Data |
| ReadTabData | Read Tab Delimited Data |
| ReadTabExpressData | Read Expression Data |
| RecordRCommand | Record R Commands |
| ReduceEdgeDensity | Reduce Edge Density |
| RemoveDuplicates | Remove Duplicates |
| RemoveMirEntry | Remove miRNA Entry |
| rescale2NewRange | Rescale to New Range |
| RowScale | Row Scale |
| scale_colours | Scale Matrix Colours |
| scale_vec_colours | Scale Vector Colours |
| SearchMultiNet | Search Multi-Network Data |
| SetCurrentDataMulti | Set Current Data Multi |
| SetPpiDb | Set Protein-Protein Interaction Db |
| SetupIndListData | Setup List Data |
| SetupItemFromList | Set up items |
| SetupItemFromPickList | Setup Item From Picklist |
| SetupMirExpressData | Setup miRNA Expression Data |
| SetupMirListData | Setup miRNA List Data |
| SetupSourceFromList | Set up source |
| SetupXenoMirListData | Setup Xeno miRNA List |
| ShowMemoryUse | Show Memory Use |
| simpleCap | Capitalize First Letter |
| sync2vecs | Synchronize Two Vectors |
| UpdateMirEntries | Update miRNA Entries |
| UpdateNetworkLayout | Update Network Layout |
| UpdateSubnetStats | Update Subnetwork Stats |
| UpdateXenoMirEntries | Update Xeno miRNA Entries |
