addTCGAdata             Creates a UI set with options to add data from
                        TCGA/Firehose
analysesServer          Server logic for the analyses
analysesUI              User interface for the data analyses
appServer               Server function
appUI                   The user interface (ui) controls the layout and
                        appearance of the app All the CSS modifications
                        are in the file "shiny/www/styles.css"
articleUI               Return the interface to display an article
basicStats              Basic statistics performed on data
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
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
createDataTab           Render a specific data tab (including data
                        table and related interface)
createDensitySparklines
                        Create density sparklines for inclusion levels
createGroup             Prepare to create group according to specific
                        details
createGroupByAttribute
                        Create groups with the indexes from the unique
                        values of a given column from a dataset
createGroupByColumn     Create groups with the indexes from the unique
                        values of a given column from a dataset
createGroupById         Create groups from a given string of rows
createGroupFromInput    Set new groups according to the user input
createJunctionsTemplate
                        Creates a template of alternative splicing
                        junctions
dataServer              Server logic of the data module
dataUI                  User interface of the data module
diffAnalyses            Perform selected statistical analyses on
                        multiple splicing events
diffSplicingEventServer
                        Server logic for the analyses of a single
                        alternative splicing event
diffSplicingEventUI     Interface for the analysis of an alternative
                        splicing event
diffSplicingServer      Server logic for the differential splicing
                        analyses
diffSplicingTableServer
                        Server logic of the exploratory differential
                        analyses
diffSplicingTableUI     Interface for differential analyses on all
                        splicing events
diffSplicingUI          User interface for the differential splicing
                        analyses
disableTab              Disable a tab from the navbar
downloadFiles           Download files to a given directory
echoProgress            Echo progress to console using 'cat'
enableTab               Enable a tab from the navbar
endProcess              Signal the program that a process has ended
ensemblToUniprot        Convert a protein's Ensembl identifier to
                        UniProt identifier
escape                  Escape symbols for use in regular expressions
export_highcharts       Add an exporting feature to a 'highcharts'
                        object
filterGroups            Filter groups with less data points than the
                        threshold
firebrowseUI            User interface of the TCGA/Firebrowse loader
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
getActiveDataset        Get selected dataset
getAssemblyVersion      Get the assembly version of a data category
getAutoNavigation       Get if history browsing is automatic
getCategories           Get available data categories
getCategory             Get selected data category
getCategoryData         Get data of selected data category
getClinicalData         Get clinical data of the data category
getClinicalMatchFrom    Get clinical matches from a given data type
getColumnsTime          Retrieve the time for given columns in a
                        clinical dataset
getCores                Get number of cores to use
getData                 Get global data
getDataRows             Get rows of a data frame between two row
                        indexes
getDifferentialAnalyses
                        Get the table of differential analyses of a
                        data category
getDifferentialAnalysesSurvival
                        Get the table of differential analyses'
                        survival data of a data category
getDownloadsFolder      Get the Downloads folder of the user
getEvent                Get selected alternative splicing event's
                        identifer
getFirehoseCohorts      Query the Firehose API for the cohorts
                        available
getFirehoseDataTypes    Get data types available from Firehose
getFirehoseDateFormat   Returns the date format used by the Firehose
                        API
getFirehoseDates        Query the Firehose API for the datestamps of
                        the data available and parse the response
getGlobal               Get data from global data
getGroupsFrom           Get groups from a given data type
getInclusionLevels      Get alternative splicing quantification of the
                        selected data category
getInclusionLevelsPCA   Get principal component analysis based on
                        inclusion levels
getJunctionQuantification
                        Get junction quantification data
getMatchingSamples      Search samples in the clinical dataset and
                        return the ones matching the given index
getNumerics             Convert a column to numeric if possible and
                        ignore given columns composed of lists
getPSIperPatient        Assign alternative splicing quantification to
                        patients based on their samples
getPatientFromSample    Match given sample identifiers and return the
                        respective row in clinical data
getPatientId            Get the identifier of patients for a given
                        category
getPrecision            Get number of decimal places
getSampleId             Get the identifier of samples for a given
                        category
getSampleInfo           Get sample information of the selected data
                        category
getSelectedGroups       Get selected groups for a given group selection
                        element
getServerFunctions      Matches server functions from a given loader
getSignificant          Get number of significant digits
getSpecies              Get the species of a data category
getSplicingEventCoordinates
                        Returns the coordinates of interest for a given
                        event type
getSplicingEventTypes   Splicing event types available
getURLtoDownload        Get the URL links to download
getUiFunctions          Matches user interface (UI) functions from a
                        given loader
getValidEvents          Filters the events with valid elements
                        according to the given validator
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
groupPerPatient         Assign one group to each patient
groupPerSample          Assign one group to each sample
groupsServer            Server function for data grouping
groupsServerOnce        Server function for data grouping (one call)
groupsUI                Creates UI elements for the grouping feature
gtexDataServer          Server logic to load GTEx data
gtexDataUI              Interface to load GTEx data
hc_scatter              Create scatter plot
hchart.survfit          Plot survival curves using Highcharts
inclusionLevelsInterface
                        Interface to quantify alternative splicing
inclusionLevelsServer   Server logic of the alternative splicing event
                        quantification module
inclusionLevelsUI       Interface of the alternative splicing event
                        quantification module
infoServer              Server logic
infoUI                  Information's user interface
insideFile              Get psichomics file inside a given directory
is.whole                Check if a number is whole
isFirehoseUp            Check if the Firehose API is running
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 cut-off
levene                  Perform Levene's test and return interface to
                        show the results
leveneTest              Levene's test
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
loadFile                Loads a file according to its format
loadFileFormats         Loads file formats
loadFirehoseData        Downloads and processes data from the Firehose
                        API and loads it into R
loadFirehoseFolders     Load Firehose folders
loadGtexData            Load GTEx data given input
loadLocalFiles          Load local files
loadedDataModal         Create a modal warning the user of already
                        loaded data
localDataServer         Server logic to load local data
localDataUI             Interface to load local data
missingDataModal        Missing information modal template
modTabPanel             Modified tabPanel function to show icon and
                        title
navSelectize            Create a special selectize input in the
                        navigatin bar
noinfo                  Interface when no information could be
                        retrieved
operateOnGroups         Set operations on groups
optimSurvDiff           Optimal survival difference given an inclusion
                        level cut-off for a specific alternative
                        splicing event
optimSurvDiffOptions    Interface for calculating optimal cut-off and
                        p-value for survival curves differences
optimalPSIcutoff        Calculate optimal alternative splicing
                        quantification cut-off to separate survival
                        curves
parseDateResponse       Parse the date from a response
parseFirehoseMetadata   Query the Firehose API for metadata and parse
                        the response
parseMatsEvent          Parse alternative splicing events from MATS
parseMatsGeneric        Parse junctions of an alternative splicing
                        event from MATS according to event type
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
parseSampleGroups       Return the type of a given sample
parseSplicingEvent      Parse an alternative splicing event based on a
                        given identifier
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
parseTcgaSampleInfo     Parse and prepare sample information from TCGA
                        samples
parseUniprotXML         Parse XML from Uniprot's RESTful service
parseUrlsFromFirehoseResponse
                        Retrieve URLs from a response to a Firehose
                        data query
parseValidFile          Parse file given a list of file formats
parseVastToolsEvent     Parses an alternative splicing event from
                        VAST-TOOLS
parseVastToolsSE        Parse junctions of an event from VAST-TOOLS
                        according to event type
pcaServer               Server logic for the principal component
                        analysis
pcaUI                   User interface of the principal component
                        analysis
performPCA              Perform principal component analysis after
                        processing missing values from data frame
plotDistribution        Plot distribution through a density plot
plotMiniSurvivalCurves
                        Perform and plot survival curves
plotPCA                 Create a scatterplot from a PCA object
plotProtein             Plot protein features
plotSurvivalCurves      Plot survival curves
plotTranscripts         Plot transcripts
plotVariance            Create the explained variance plot
prepareAnnotationFromEvents
                        Prepare annotation from alternative splicing
                        events
prepareFirehoseArchives
                        Prepares Firehose archives in a given directory
processButton           Style button used to initiate a process
processDatasetNames     Process dataset names
processSurvData         Process survival data to calculate survival
                        curves
processSurvTerms        Process survival curves terms to calculate
                        survival curves
processSurvival         Check if survival analyses successfully
                        completed or returned errors
psichomics              Start graphical interface of PSICHOMICS
pubmedUI                Return the interface of relevant PubMed
                        articles for a given gene
quantifySplicing        Quantify alternative splicing events
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
queryFirehoseData       Query the Firehose API for TCGA data
queryPubMed             Query the PubMed REST API
queryUniprot            Query the Uniprot REST API
readFile                Load local file
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
rm.null                 Filter NULL elements from vector or list
roundDigits             Round by the given number of digits
rowVar                  Sample variance by row
selectGroupsServer      Group selection logic
selectGroupsUI          Group selection interface
setActiveDataset        Set active dataset
setAssemblyVersion      Set the assembly version of a data category
setAutoNavigation       Set if history browsing is automatic
setCategory             Set data category
setClinicalMatchFrom    Set clinical matches from a given data type
setCores                Set number of cores
setData                 Set data of the global data
setDifferentialAnalyses
                        Set the table of differential analyses of a
                        data category
setDifferentialAnalysesSurvival
                        Set the table of differential analyses'
                        survival data of a data category
setEvent                Set event
setFirehoseData         Set data from Firehose
setGlobal               Set element as globally accessible
setGroupsFrom           Set groups from a given data type
setInclusionLevels      Set inclusion levels for a given data category
setInclusionLevelsPCA   Get principal component analysis based on
                        inclusion levels
setLocalData            Load local files
setPatientId            Set the identifier of patients for a data
                        category
setPrecision            Set number of decimal places
setSampleId             Set the identifier of samples for a data
                        category
setSampleInfo           Set sample information for a given data
                        category
setSignificant          Set number of significant digits
setSpecies              Set the species of a data category
setURLtoDownload        Set URL links to download
settingsServer          Server logic of the settings
settingsUI              User interface of the settings
showAlert               Show an alert
showGroupsTable         Present groups table
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
survdiff.survTerms      Test difference between two or more survival
                        curves using processed survival terms
survfit.survTerms       Compute estime of a survival curve using
                        processed survival terms
survivalServer          Server logic of survival analysis
survivalUI              User interface of survival analysis
tabDataset              Creates a tabPanel template for a datatable
                        with a title and description
templateServer          Server logic of template
templateUI              User interface of template
testSurvival            Test the survival difference between survival
                        groups
testSurvivalCutoff      Test the survival difference between two
                        survival groups given a cutoff
textSuggestions         Create script for autocompletion of text input
timePerPatient          Get all columns matching a given string and
                        return a single vector with the max time for
                        each patient if available
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
updateProgress          Update a progress object
vennEvents              Compare the number of events from the different
                        programs in a Venn diagram
wilcox                  Perform Wilcoxon analysis and return interface
                        to show the results
