A B C D E F G H I J K L M N O P Q R S T U V W
| addObjectAttrs | Set attributes to an object |
| addTCGAdata | Creates a UI set with options to add data from TCGA/Firebrowse |
| analysesPlotSet | Set of functions to plot differential analyses |
| analysesServer | Server logic |
| analysesTableSet | Set of functions to render data table for differential analyses |
| analysesUI | User interface |
| appendNewGroups | Append new groups to already existing groups |
| appServer | Server logic |
| appUI | User interface |
| areSplicingEvents | Check if string identifies splicing events |
| articleUI | Return the interface to display an article |
| ASquantFileInput | File input for alternative splicing quantification |
| assignColours | Assign colours to groups |
| assignValuePerPatient | Assign average sample values to their corresponding patients |
| assignValuePerSubject | Assign average sample values to their corresponding patients |
| basicStats | Basic statistics performed on data |
| blendColours | Blend two HEX colours |
| browserHistory | Enable history navigation |
| bsModal2 | Modified version of 'shinyBS::bsModal' |
| calculateInclusionLevels | Calculate inclusion levels using alternative splicing event annotation and junction quantification for many samples |
| calculateLoadingsContribution | Calculate the contribution of PCA loadings to the selected principal components |
| checkFileFormat | Checks the format of a file |
| checkFirebrowse | Return an user interface depending on the status of the Firebrowse API |
| checkIntegrity | Compute the 32-byte 'MD5' hashes of one or more files and check with given 'md5' file |
| checkSurvivalInput | Prepare survival terms in case of valid input |
| closeProgress | Close the progress even if there's an error |
| clusterICAset | Server logic for clustering ICA data |
| clusterSet | Server logic for clustering PCA data |
| colourInputMod | Modified colour input with 100% width |
| correlateGEandAS | Correlate gene expression data against alternative splicing quantification |
| correlationServer | Server logic |
| correlationUI | User interface |
| createDataTab | Render a specific data tab (including data table and related interface) |
| createDensitySparklines | Create density sparklines for inclusion levels |
| createEventPlotting | Create plot for events |
| createGroup | Prepare to create group according to specific details |
| createGroupByAttribute | Split elements into groups based on a given column of a dataset |
| createGroupByColumn | Split elements into groups based on a given column of a dataset |
| createGroupById | Create groups based on given row indexes or identifiers |
| createGroupFromInput | Set new groups according to the user input |
| createJunctionsTemplate | Creates a template of alternative splicing junctions |
| createOptimalSurvData | Create survival data based on a PSI cutoff |
| createSparklines | Create sparkline charts to be used in a data table |
| dataServer | Server logic |
| dataUI | User interface |
| diffAnalyses | Perform statistical analyses |
| diffAnalysis | Perform statistical analyses |
| diffExpressionEventServer | Server logic |
| diffExpressionEventUI | User interface |
| diffExpressionServer | Server logic |
| diffExpressionSet | Set of functions to perform differential analyses |
| diffExpressionTableServer | Server logic |
| diffExpressionTableUI | User interface |
| diffExpressionUI | User interface |
| diffSplicingEventServer | Server logic |
| diffSplicingEventUI | User interface |
| diffSplicingServer | Server logic |
| diffSplicingSet | Set of functions to perform differential analyses |
| diffSplicingTableServer | Server logic |
| diffSplicingTableUI | User interface |
| diffSplicingUI | User interface |
| dimReductionServer | Server logic |
| dimReductionUI | User interface |
| disableTab | Enable or disable a tab from the 'navbar' |
| display | Display characters in the command-line |
| downloadFiles | Download files to a given directory |
| enableTab | Enable or disable a tab from the 'navbar' |
| endProcess | Signal the program that a process has ended |
| ensemblToUniprot | Convert an Ensembl identifier to the respective UniProt identifier |
| errorAlert | Show or remove an alert |
| errorDialog | Alert in the style of a dialogue box with a button |
| errorModal | Style and show a modal |
| escape | Escape symbols for use in regular expressions |
| eventPlotOptions | Options for event plotting |
| export_highcharts | Add an exporting feature to a 'highcharts' object |
| fileBrowser | Interactive folder selection using a native dialogue |
| fileBrowserInput | File browser input |
| filterGroups | Filter groups with less data points than the threshold |
| findASeventsFromGene | Find splicing events based on given genes |
| firebrowseServer | Server logic |
| firebrowseUI | User interface |
| fisher | Perform Fisher's exact test and return interface to show the results |
| fligner | Perform Fligner-Killeen test and return interface to show the results |
| geneExprFileInput | File input for gene expression |
| geneExprSurvSet | Logic set to perform survival analysis based on gene expression cut-offs |
| geNormalisationFilteringInterface | Interface to normalise and filter gene expression |
| geNormalisationFilteringServer | Server logic |
| geNormalisationFilteringUI | User interface |
| getActiveDataset | Get or set globally accessible elements |
| getAnnotationName | Get or set globally accessible elements |
| getASevent | Get or set globally accessible elements |
| getASevents | Get or set globally accessible elements |
| getAssemblyVersion | Get or set globally accessible elements |
| getAttributesTime | Retrieve the time for given columns in a clinical dataset |
| getAutoNavigation | Get or set globally accessible elements |
| getCategories | Get or set globally accessible elements |
| getCategory | Get or set globally accessible elements |
| getCategoryData | Get or set globally accessible elements |
| getClinicalData | Get or set globally accessible elements |
| getClinicalDataForSurvival | Retrieve clinical data based on attributes required for survival analysis |
| getClinicalMatchFrom | Get or set clinical matches from a given data type |
| getColumnsTime | Retrieve the time for given columns in a clinical dataset |
| getCores | Get or set globally accessible elements |
| getCorrelation | Get or set globally accessible elements |
| getData | Get global data |
| getDataRows | Get rows of a data frame between two row indexes |
| getDifferentialExpression | Get or set differential expression' elements for a data category |
| getDifferentialExpressionColumns | Get or set differential expression' elements for a data category |
| getDifferentialExpressionFiltered | Get or set differential expression' elements for a data category |
| getDifferentialExpressionResetPaging | Get or set differential expression' elements for a data category |
| getDifferentialExpressionSurvival | Get or set differential expression' elements for a data category |
| getDifferentialSplicing | Get or set differential splicing' elements for a data category |
| getDifferentialSplicingColumns | Get or set differential splicing' elements for a data category |
| getDifferentialSplicingFiltered | Get or set differential splicing' elements for a data category |
| getDifferentialSplicingResetPaging | Get or set differential splicing' elements for a data category |
| getDifferentialSplicingSurvival | Get or set differential splicing' elements for a data category |
| getDownloadsFolder | Get the Downloads folder of the user |
| getEvent | Get or set globally accessible elements |
| getFirebrowseCohorts | Query the Firebrowse web API for available cohorts |
| getFirebrowseDataTypes | Get data types available from Firebrowse |
| getFirebrowseDateFormat | Returns the date format used by the Firebrowse web API |
| getFirebrowseDates | Query the Firebrowse web API for the available data datestamps |
| getFirehoseCohorts | Query the Firebrowse web API for available cohorts |
| getFirehoseDataTypes | Get data types available from Firebrowse |
| getFirehoseDates | Query the Firebrowse web API for the available data datestamps |
| getGeneExpression | Get or set globally accessible elements |
| getGenes | Get or set globally accessible elements |
| getGenesFromSplicingEvents | Retrieve genes based on given alternative splicing events |
| getGlobal | Get or set globally accessible elements |
| getGroupIndependenceTesting | Get or set globally accessible elements |
| getGroups | Get or set groups |
| getGTExTissues | Get GTEx tissues from given GTEx sample attributes |
| getGtexTissues | Get GTEx tissues from given GTEx sample attributes |
| getHidden | Get or set hidden globally accessible elements |
| getHighlightedPoints | Get or set points or regions for plots |
| getICA | Get or set globally accessible elements |
| getInclusionLevels | Get or set globally accessible elements |
| getJunctionQuantification | Get or set globally accessible elements |
| getLabelledPoints | Get or set points or regions for plots |
| getMatchingSamples | Get samples matching the given patients |
| getNumerics | Convert a column to numeric if possible and ignore given columns composed of lists |
| getPatientAttributes | Get or set globally accessible elements |
| getPatientFromSample | Get patients from given samples |
| getPatientId | Get or set globally accessible elements |
| getPCA | Get or set globally accessible elements |
| getPrecision | Get or set globally accessible elements |
| getPSIperPatient | Assign average sample values to their corresponding patients |
| getSampleAttributes | Get or set globally accessible elements |
| getSampleFromPatient | Get samples matching the given patients |
| getSampleFromSubject | Get samples matching the given patients |
| getSampleId | Get or set globally accessible elements |
| getSampleInfo | Get or set globally accessible elements |
| getSelectedGroups | Group selection |
| getSelectedPoints | Get or set points or regions for plots |
| getServerFunctions | Matches server functions from a given loader |
| getSignificant | Get or set globally accessible elements |
| getSpecies | Get or set globally accessible elements |
| getSplicingEventCoordinates | Returns the coordinates of interest for a given event type |
| getSplicingEventFromGenes | Retrieve alternative splicing events based on given genes |
| getSplicingEventTypes | Splicing event types available |
| getSubjectFromSample | Get patients from given samples |
| getTCGAcohorts | Query the Firebrowse web API for available cohorts |
| getTCGAdates | Query the Firebrowse web API for the available data datestamps |
| getUiFunctions | Matches user interface (UI) functions from a given loader |
| getURLtoDownload | Get or set globally accessible elements |
| getValidEvents | Filters the events with valid elements according to the given validator |
| getValuePerPatient | Assign average sample values to their corresponding patients |
| getValuePerSubject | Assign average sample values to their corresponding patients |
| getZoom | Get or set points or regions for plots |
| ggplotAuxServer | Logic set to create an interactive ggplot |
| ggplotServer | Logic set to create an interactive ggplot |
| ggplotTooltip | Create the interface for the tooltip of a plot |
| ggplotUI | Interface for interactive ggplot |
| globalSelectize | Create a selectize input available from any page |
| groupByAttribute | User interface to group by attribute |
| groupByExpression | User interface to group by subset expression |
| groupByGrep | User interface to group by grep expression |
| groupById | User interface to group by row |
| groupManipulation | Logic server to manipulate data grouping |
| groupManipulationInput | Interface to manipulate data grouping |
| groupPerElem | Assign one group to each element |
| groupPerPatient | Assign one group to each element |
| groupPerSample | Assign one group to each element |
| groupsServer | Server logic |
| groupsServerOnce | Server function for data grouping (one call) |
| groupsUI | User interface |
| gtexDataServer | Server logic |
| gtexDataUI | User interface |
| hchart.survfit | Plot survival curves using Highcharts |
| hc_scatter | Create scatter plot |
| helpServer | Server logic |
| helpUI | User interface |
| icaServer | Server logic |
| icaUI | User interface |
| inclusionLevelsInterface | Interface to quantify alternative splicing |
| inclusionLevelsServer | Server logic |
| inclusionLevelsUI | User interface |
| infoModal | Style and show a modal |
| infoServer | Server logic |
| infoUI | User interface |
| inlineDialog | Alert in the style of a dialogue box with a button |
| insideFile | Get psichomics file inside a given directory |
| is.whole | Check if a number is whole |
| isFile | Check if files exist |
| isFirebrowseUp | Check whether the Firebrowse web API is running |
| isFirehoseUp | Check whether the Firebrowse web API is running |
| isRStudioServer | Check if running in RStudio Server |
| joinEventsPerType | Full outer join all given events based on select columns |
| junctionString | String used to search for matches in a junction quantification file |
| kruskal | Perform Kruskal's test and return interface to show the results |
| labelBasedOnCutoff | Label groups based on a given cutoff |
| levene | Perform Levene's test and return interface to show the results |
| leveneTest | Levene's test |
| linkToArticle | Interface that directs users to original article |
| linkToRunJS | Link to run arbitrary JavaScript code |
| listAllAnnotations | List alternative splicing annotation files available, as well as custom annotation |
| listSplicingAnnotations | List the alternative splicing annotation files available |
| loadAnnotation | Load alternative splicing annotation from 'AnnotationHub' |
| loadBy | Check if a given function should be loaded by the calling module |
| loadCustomSplicingAnnotationSet | Set of functions to load a custom alternative splicing annotation |
| loadedDataModal | Create a modal warning the user of already loaded data |
| loadFile | Loads a file according to its format |
| loadFileFormats | Loads file formats |
| loadFirebrowseData | Downloads and processes data from the Firebrowse web API and loads it into R |
| loadFirebrowseFolders | Load Firebrowse folders |
| loadFirehoseData | Downloads and processes data from the Firebrowse web API and loads it into R |
| loadFirehoseFolders | Load Firebrowse folders |
| loadGeneExpressionSet | Set of functions to load splicing quantification |
| loadGtexData | Load GTEx data |
| loadGtexDataShiny | Shiny wrapper to load GTEx data |
| loadGTExFile | Load GTEx file |
| loadGtexFile | Load GTEx file |
| loadLocalFiles | Load local files |
| loadRequiredData | Missing information modal template |
| loadSplicingQuantificationSet | Set of functions to load splicing quantification |
| loadSRAproject | Download and load SRA projects |
| loadTCGAdata | Downloads and processes data from the Firebrowse web API and loads it into R |
| loadTCGAfolders | Load Firebrowse folders |
| loadTCGAsampleMetadata | Prepare TCGA sample metadata from loaded datasets |
| localDataServer | Server logic |
| localDataUI | User interface |
| matchGroupPatientsAndSamples | Match patients and samples in a group |
| matchSplicingEventsWithGenes | Match splicing events with respective genes |
| missingDataGuide | Missing information modal template |
| missingDataModal | Missing information modal template |
| modTabPanel | Modified 'tabPanel' function to show icon and title |
| navSelectize | Create a special selectize input in the navigation bar |
| noinfo | Interface when no information could be retrieved |
| normaliseGeneExpression | Filter and normalise gene expression |
| operateOnGroups | Set operations on groups |
| optimalPSIcutoff | Calculate optimal data cutoff that best separates survival curves |
| optimalSurvivalCutoff | Calculate optimal data cutoff that best separates survival curves |
| optimSurvDiffSet | Optimal survival difference given an inclusion level cutoff for a specific alternative splicing event |
| parseCategoricalGroups | Parse categorical columns in a data frame |
| parseDateResponse | Parse the date from a response |
| parseFirebrowseMetadata | Query the Firebrowse web API for metadata |
| parseFirehoseMetadata | Query the Firebrowse web API for metadata |
| parseMatsA3SS | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsA5SS | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsAFE | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsALE | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsAnnotation | Get events from alternative splicing annotation |
| parseMatsEvent | Parse alternative splicing events from MATS |
| parseMatsGeneric | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsMXE | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsRI | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsSE | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMisoA3SS | Parse junctions of an event from MISO according to event type |
| parseMisoA5SS | Parse junctions of an event from MISO according to event type |
| parseMisoAFE | Parse junctions of an event from MISO according to event type |
| parseMisoALE | Parse junctions of an event from MISO according to event type |
| parseMisoAnnotation | Get events from alternative splicing annotation |
| parseMisoEvent | Parse an alternative splicing event from MISO |
| parseMisoEventID | Match MISO's splicing event IDs with the IDs present in the alternative splicing annotation file and get events in a data frame |
| parseMisoGeneric | Parse junctions of an event from MISO according to event type |
| parseMisoId | Parse MISO's alternative splicing event identifier |
| parseMisoMXE | Parse junctions of an event from MISO according to event type |
| parseMisoRI | Parse junctions of an event from MISO according to event type |
| parseMisoSE | Parse junctions of an event from MISO according to event type |
| parseMisoTandemUTR | Parse junctions of an event from MISO according to event type |
| parseSampleGroups | Return the type of a given sample |
| parseSplicingEvent | Parse an alternative splicing event based on a given identifier |
| parseSuppaA3SS | Parse junctions of an event from SUPPA |
| parseSuppaA5SS | Parse junctions of an event from SUPPA |
| parseSuppaAFE | Parse junctions of an event from SUPPA |
| parseSuppaALE | Parse junctions of an event from SUPPA |
| parseSuppaAnnotation | Get events from alternative splicing annotation |
| parseSuppaEvent | Parses splicing events of a specific event type from SUPPA |
| parseSuppaGeneric | Parse junctions of an event from SUPPA |
| parseSuppaMXE | Parse junctions of an event from SUPPA |
| parseSuppaRI | Parse junctions of an event from SUPPA |
| parseSuppaSE | Parse junctions of an event from SUPPA |
| parseTCGAmetadata | Query the Firebrowse web API for metadata |
| parseTCGAsampleInfo | Parse sample information from TCGA samples |
| parseTcgaSampleInfo | Parse sample information from TCGA samples |
| parseUniprotXML | Parse XML from UniProt's RESTful service |
| parseUrlsFromFirebrowseResponse | Retrieve URLs from a response to a Firebrowse data query |
| parseUrlsFromFirehoseResponse | Retrieve URLs from a response to a Firebrowse data query |
| parseValidFile | Parse file given a list of file formats |
| parseVastToolsA3SS | Parse junctions of an event from VAST-TOOLS according to event type |
| parseVastToolsA5SS | Parse junctions of an event from VAST-TOOLS according to event type |
| parseVastToolsAnnotation | Get events from alternative splicing annotation |
| parseVastToolsEvent | Parses an alternative splicing event from VAST-TOOLS |
| parseVastToolsRI | Parse junctions of an event from VAST-TOOLS according to event type |
| parseVastToolsSE | Parse junctions of an event from VAST-TOOLS according to event type |
| patientMultiMatchWarning | Helper text to explain what happens when a patient matches multiple samples when performing survival analysis |
| pcaServer | Server logic |
| pcaUI | User interface |
| performICA | Perform independent component analysis after processing missing values |
| performPCA | Perform principal component analysis after processing missing values |
| plot.GEandAScorrelation | Plot correlations |
| plotClusters | Add clusters to 'highchart' object |
| plotCorrelation | Plot correlations |
| plotDensity | Plot distribution through a density plot |
| plotDistribution | Plot distribution through a density plot |
| plotGroupIndependence | Plot -log10(p-values) of the results obtained after multiple group independence testing |
| plotICA | Create multiple scatterplots from ICA |
| plotPCA | Create a scatterplot from a PCA object |
| plotPointsStyle | Interface to modify the style of the plot points |
| plotProtein | Plot protein features |
| plotSingleICA | Create a scatterplot for ICA |
| plotSurvivalCurves | Plot survival curves |
| plottableXranges | HTML code to plot a X-ranges series |
| plotTranscripts | Plot transcripts |
| plotVariance | Create the explained variance plot |
| prepareAnnotationFromEvents | Prepare annotation from alternative splicing events |
| prepareEventPlotOptions | Prepare event plot options |
| prepareFileBrowser | Prepare file browser dialogue and update the input's value accordingly to selected file or directory |
| prepareFirebrowseArchives | Prepares Firebrowse archives in a given directory |
| prepareFirehoseArchives | Prepares Firebrowse archives in a given directory |
| prepareGeneQuant | Prepare files to be loaded into psichomics |
| prepareGeneQuantSTAR | Prepare files to be loaded into psichomics |
| prepareJunctionQuant | Prepare files to be loaded into psichomics |
| prepareJunctionQuantSTAR | Prepare files to be loaded into psichomics |
| prepareSRAmetadata | Prepare files to be loaded into psichomics |
| prepareTCGAarchives | Prepares Firebrowse archives in a given directory |
| prepareWordBreak | Create word break opportunities (for HTML) using given characters |
| processButton | Style button used to initiate a process |
| processDatasetNames | Process dataset names |
| processSurvData | Process survival data to calculate survival curves |
| processSurvival | Check if survival analyses successfully completed or returned errors |
| processSurvTerms | Process survival curves terms to calculate survival curves |
| psichomics | Start graphical interface of psichomics |
| pubmedUI | Return the interface of relevant PubMed articles for a given gene |
| quantifySplicing | Quantify alternative splicing events |
| quantifySplicingSet | Set of functions to quantify alternative splicing |
| queryEnsembl | Query the Ensembl REST API |
| queryEnsemblByEvent | Query information from Ensembl by a given alternative splicing event |
| queryEnsemblByGene | Query information from Ensembl by a given gene |
| queryFirebrowseData | Query the Firebrowse web API for TCGA data |
| queryFirehoseData | Query the Firebrowse web API for TCGA data |
| queryPubMed | Query the PubMed REST API |
| queryUniprot | Query the UniProt REST API |
| readAnnot | Read custom or remote annotation |
| readFile | Load local file |
| recountDataServer | Server logic |
| recountDataUI | User interface |
| reduceDimensionality | Reduce dimensionality after processing missing values from data frame |
| removeAlert | Show or remove an alert |
| renameDuplicated | Rename vector to avoid duplicated values with another vector |
| renameGroups | Rename duplicated names from a new group |
| renderDataTableSparklines | Render a data table with sparkline HTML elements |
| renderGeneticInfo | Render genetic information |
| renderGroupInterface | Render group interface |
| renderProteinInfo | Render protein information |
| rm.null | Filter NULL elements from vector or list |
| roundDigits | Round by the given number of digits |
| roundMaxUp | Round down/up the minimum/maximum value |
| roundMinDown | Round down/up the minimum/maximum value |
| rowMeans | Calculate mean for each row of a matrix |
| rowVars | Calculate variance for each row of a matrix |
| selectGroupsServer | Group selection |
| selectGroupsUI | Group selection |
| selectizeGeneInput | Create input to select a gene |
| setActiveDataset | Get or set globally accessible elements |
| setAnnotationName | Get or set globally accessible elements |
| setASevent | Get or set globally accessible elements |
| setAssemblyVersion | Get or set globally accessible elements |
| setAutoNavigation | Get or set globally accessible elements |
| setCategory | Get or set globally accessible elements |
| setClinicalMatchFrom | Get or set clinical matches from a given data type |
| setCores | Get or set globally accessible elements |
| setCorrelation | Get or set globally accessible elements |
| setData | Get or set globally accessible elements |
| setDataTable | Get or set globally accessible elements |
| setDifferentialExpression | Get or set differential expression' elements for a data category |
| setDifferentialExpressionColumns | Get or set differential expression' elements for a data category |
| setDifferentialExpressionFiltered | Get or set differential expression' elements for a data category |
| setDifferentialExpressionResetPaging | Get or set differential expression' elements for a data category |
| setDifferentialExpressionSurvival | Get or set differential expression' elements for a data category |
| setDifferentialSplicing | Get or set differential splicing' elements for a data category |
| setDifferentialSplicingColumns | Get or set differential splicing' elements for a data category |
| setDifferentialSplicingFiltered | Get or set differential splicing' elements for a data category |
| setDifferentialSplicingResetPaging | Get or set differential splicing' elements for a data category |
| setDifferentialSplicingSurvival | Get or set differential splicing' elements for a data category |
| setEvent | Get or set globally accessible elements |
| setFirebrowseData | Set data from Firebrowse |
| setGlobal | Get or set globally accessible elements |
| setGroupIndependenceTesting | Get or set globally accessible elements |
| setGroups | Get or set groups |
| setHidden | Get or set hidden globally accessible elements |
| setHighlightedPoints | Get or set points or regions for plots |
| setICA | Get or set globally accessible elements |
| setInclusionLevels | Get or set globally accessible elements |
| setLabelledPoints | Get or set points or regions for plots |
| setLocalData | Load local files |
| setMultipleFilesData | Load local files |
| setNormalisedGeneExpression | Get or set globally accessible elements |
| setOperation | Perform set operations on selected groups |
| setOperationIcon | Create an icon based on set operations |
| setPCA | Get or set globally accessible elements |
| setPrecision | Get or set globally accessible elements |
| setSampleInfo | Get or set globally accessible elements |
| setSelectedPoints | Get or set points or regions for plots |
| setSignificant | Get or set globally accessible elements |
| setSpecies | Get or set globally accessible elements |
| setURLtoDownload | Get or set globally accessible elements |
| setZoom | Get or set points or regions for plots |
| showAlert | Show or remove an alert |
| showGroupsTable | Present groups table |
| sidebar | Sidebar without a well |
| signifDigits | Get number of significant digits |
| singleDiffAnalyses | Perform statistical analysis on a given splicing event |
| sortCoordinates | Sort coordinates for some event types |
| spearman | Perform Spearman's test and return interface to show the results |
| startProcess | Signal the program that a process is starting |
| startProgress | Create a progress object |
| styleModal | Style and show a modal |
| subsetGeneExpressionFromMatchingGenes | Subset gene expression based on (full or partial) matching genes |
| survdiff.survTerms | Test differences between survival curves |
| survfit.survTerms | Compute estimates of survival curves |
| survivalServer | Server logic |
| survivalUI | User interface |
| tabDataset | Creates a 'tabPanel' template for a 'datatable' with a title and description |
| table2html | Create HTML table from data frame or matrix |
| tableRow | Create a row for a HTML table |
| templateServer | Server logic |
| templateUI | User interface |
| testGroupIndependence | Multiple independence tests between reference groups and list of groups |
| testSingleIndependence | Multiple independence tests between a reference group and list of groups |
| testSurvival | Test the survival difference between groups of patients |
| testSurvivalCutoff | Test the survival difference between two survival groups given a cutoff |
| textSuggestions | Create script for auto-completion of text input |
| toJSarray | Convert vector of values to JavaScript array |
| transformData | Transform data in data frame |
| transformOptions | Show variable transformation(s) |
| transformValues | Transform values as per a given type of transformation |
| trimWhitespace | Trims whitespace from a word |
| ttest | Perform unpaired t-test analysis and return interface to show the results |
| uniqueBy | Check unique rows of a data frame based on a set of its columns |
| updateClinicalParams | Update available clinical attributes when the clinical data changes |
| updateFileBrowserInput | Change the value of a fileBrowserInput on the client |
| updateProgress | Update a progress object |
| vennEvents | Compare the number of events from the different programs in a Venn diagram |
| warningAlert | Show or remove an alert |
| warningDialog | Alert in the style of a dialogue box with a button |
| warningModal | Style and show a modal |
| wilcox | Perform Wilcoxon analysis and return interface to show the results |