bhCorrect | Helper function to return a Benjamini-Hochberg (BH) corrected... |
buildFrequencyTables | Return all analytes that map to unique pathways in a... |
checkIdPrefixes | Check for id prefixes By default, the function checks on... |
chemicalClassEnrichment | Returns chemical class information comparing a metabolite... |
chemicalClassSurvey | Returns chemical class information comparing a metabolite... |
chemicalClassSurveyRampIdsConn | chemicalClassSurveyRampIdsConn2 is a helper function that... |
chemicalClassSurveyRampIdsFullPopConn | chemicalClassSurveyRampIdsFullPopConn2 is a helper function... |
cleanup | Generic function for removing RaMP identifiers and making... |
compute_overlap_matrix | Compute overlaping matrix based on given list return by... |
connectToRaMP | Connect to RaMP database (requires mysql password when... |
FilterFishersResults | Filter pathways by p-value cutoff for display and clustering |
findAnalyteHasPathway | Find table of analyte has pathway from given pathway IDs... |
findCluster | Perform fuzzy multiple linkage partitioning clustering on... |
find_duplicate_pathways | Return list of duplicate Wikipathway IDs from Reactome. This... |
findDuplicatePathways | Return list of duplicate Wikipathway IDs from Reactome. This... |
getAnalyteFromPathway | Use fast search algorithm to find all pathways from given... |
getChemicalProperties | Returns chemical properties given a metabolite list |
getCurrentRaMPSourceDBVersions | Retrieve versions of each database within the current version... |
getCurrentRaMPVersion | Retrieve RaMP version |
getCustomPathwayFromAnalyte | Reads an excel file containing metabolite and gene... |
getEntityCountsFromSourceDBs | Retrieve counts of entitites (e.g. Metabolites, Pathways,... |
getMetabChemClass | Returns chemical classes for classType |
getMetabClassDataSources | Returns class data sources for metabolites |
getMetabClassTypes | Returns class categories for metabolites |
getMetaFromOnto | function that query database to find analytes in given... |
getOntoFromMeta | Function that query database to find ontology information... |
getOntologies | Returns list of available ontologies from database |
getPathwayFromAnalyte | Function that search analytes (gene or compounds) or a list... |
getPathwayNameList | Retrieve list of pathway names |
getPrefixesFromAnalytes | Query to retrieve database ID prefixes for analyte types |
getRaMPAnalyteIntersections | Retrieve RaMP Analyte Source Intersections, these indicate... |
getRaMPInfoFromAnalytes | Internal function for extracting annotations, used by pathway... |
getRampSourceInfoFromAnalyteIDs | getRampSourceInfoFromAnalyteIDs Utility method to extract... |
getReactionsForAnalytes | getReactionsForAnalytes |
getReactionsForRaMPCompoundIds | getReactionsForRaMPCompoundIds returns reactions for a... |
getReactionsForRaMPGeneIds | getReactionsForRaMPGeneIds returns reactions for a collection... |
getTotalFoundInCategories | Utility method to return metabolite counts found in compound... |
listToQueryString | listToQueryString utility method to convert an id list to a... |
pathwayResultsPlot | Cluster and plot significant pathways by FDR-adjusted pval |
plotCataNetwork | Plots a network based on gene-metabolite relationships |
processData | processData function generates pathway RampId frequency (gene... |
queryReport | queryReport is a helper function to report on the number of... |
rampFastCata | Retrieves analytes that involved in same reaction as input... |
rampFastCataOriginal | Retrieves analytes that involved in same reaction as input... |
rampFastPathFromSource | Fast search given a list of metabolites source Id |
rampFindClassInfoFromSourceId | Get class info for an input of metabolite source Ids |
rampFindSourceFromId | Find all source from given list of RaMP Ids |
rampFindSourceRampId | Find rampId from given source ID The rampId can be plugged in... |
rampFindSynonymFromSynonym | Find all synonym from a given metabolite's name This function... |
runCombinedFisherTest | Do fisher test for only one pathway from search result... |
runFisherTest | Do fisher test for only one pathway from search result... |
segregateDataBySource | Separate input ids into lists based on database of origin |
setConnectionToRaMP | Set Connection Parameters or RaMP |
updateOverlapMatrices | Update and save the overlap matrices based on current version... |
updateOverlapMatrix | Update the overlap matrix for store in the shiny app... |
write_FishersResults | Function that writes Fishers Test results, after clustering... |
writePathwaysToCSV | Function that writes output from getPathwayFromAnalyte() to a... |
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