Man pages for hyginn/BCB420.2019.ESA
Exploratory Systems Analysis Tools
| clusterSystems | Cluster Systems |
| complexExpHeatmap | 'complexExpHeatmap' Heatmap of the complex subunits... |
| domainEnrichment | Domain enrichment in a desired system. |
| EnrichDepletTF | EnrichDepletTF. |
| expr_dist | Expression Distance. |
| exProf | Gene Expression Profile. |
| fetchComponents | 'fetchComponents' get all gene symbols in a system. |
| fetchData | 'fetchData' read a prepared dataset from a repository. |
| findSTRINGKnodes | 'findSTRINGKnodes' output the K node values for vertices in... |
| genePairsShuffle | 'genePairsShuffle' Generate Coexpression correlation... |
| getCoExpProfile | 'getCoExpProfile' Generate a coexpression profile |
| getComplexmyQNXP | 'getComplexmyQNXP' Extract expression profile for the complex... |
| getGeneticInteractome | getGeneticInteractome |
| getpValue | 'getpValue' calculate p-Value |
| getSysInteractions | getSysInteractions |
| hypothesize | hypothesize |
| installHumanGenomeAnnotation | 'installHumanGenomeAnnotation' install Human genome... |
| jaccard_dist | Jaccard Distance. |
| makeEMAP | Generate the genetic interpretation map of BioGrid GGI tags... |
| makeGMAP | Generate the genetic interpretation map of BioGrid GGI tags. |
| makeSeq | 'makeSeq' output a random DNA sequence. |
| myScatterPlot | 'myScatterPlot()' Expression and Semantic Similarity |
| pairExpHist | 'pairExpHist' Generate distribution of coexpression... |
| PathwayEnrichment | 'PathwayEnrichment' a function that perform a pathway... |
| processmyQNXP | 'processmyQNXP' Load and process expression-profiles |
| rptGC | rptGC.R |
| STRINGExplore | STRINGExplore |
| SyDBgetIDforKey | 'SyDBgetIDforKey' fetch an ID from a systems database. |
| SyDBgetRootSysIDs | 'SyDBgetRootSysIDs' fetch root-system IDs from a systems... |
| SyDBgetSysSymbols | 'SyDBgetSysSymbols' fetch root-system IDs from a systems... |
| SyDBgetValForID | 'SyDBgetValForID' fetch an an attribute value for an ID from... |
| SyDBinvalid | 'SyDBinvalid' validate a systems database. |
| SyDBTree | 'SyDBTree' print a (sub)system as a tree |
| sysCorGenes | sysUpCorGenes. |
| sysExProf | sysExProf. |
| sysGTRDgenes | sysGTRDgenes. |
| sysGTRDtf | sysGTRDtf. |
| System_Expression | System level expression values. |
| tf_dist | Transcription Factor Distance |
| visualizeInteractions | visualizeInteractions |
