ASquantFileInput        File input for alternative splicing
                        quantification
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
analysesTableSet        Set of functions to render data table for
                        differential analyses
appServer               Server logic
appUI                   User interface
appendNewGroups         Append new groups to already existing groups
areSplicingEvents       Check if string identifies splicing events
articleUI               Return the interface to display an article
assignColours           Assign colours to groups
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
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
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
diffAnalyses            Perform statistical analyses
diffExpressionSet       Set of functions to perform differential
                        analyses
diffSplicingSet         Set of functions to perform differential
                        analyses
disableTab              Enable or disable a tab from the 'navbar'
display                 Display characters in the command-line
downloadFiles           Download files to a given directory
endProcess              Signal the program that a process has ended
ensemblToUniprot        Convert an Ensembl identifier to the respective
                        UniProt identifier
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
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
geNormalisationFilteringInterface
                        Interface to normalise and filter gene
                        expression
geneExprFileInput       File input for gene expression
geneExprSurvSet         Logic set to perform survival analysis based on
                        gene expression cut-offs
getASevent              Get or set globally accessible elements
getASevents             Get or set globally accessible elements
getAttributesTime       Retrieve the time for given columns in a
                        clinical dataset
getClinicalDataForSurvival
                        Retrieve clinical data based on attributes
                        required for survival analysis
getClinicalMatchFrom    Get or set clinical matches from a given data
                        type
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
getDifferentialSplicing
                        Get or set differential splicing' elements for
                        a data category
getDownloadsFolder      Get the Downloads folder of the user
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
getGenes                Get or set globally accessible elements
getGenesFromSplicingEvents
                        Retrieve genes based on given alternative
                        splicing events
getGlobal               Get or set globally accessible elements
getGroups               Get or set groups
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
getMatchingSamples      Get samples matching the given patients
getNumerics             Convert a column to numeric if possible and
                        ignore given columns composed of lists
getPatientFromSample    Get patients from given samples
getServerFunctions      Matches server functions from a given loader
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
getUiFunctions          Matches user interface (UI) functions from a
                        given loader
getValidEvents          Filters the events with valid elements
                        according to the given validator
getValuePerPatient      Assign average sample values to their
                        corresponding patients
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
groupsServerOnce        Server function for data grouping (one call)
hc_scatter              Create scatter plot
hchart.survfit          Plot survival curves using Highcharts
inclusionLevelsInterface
                        Interface to quantify alternative splicing
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
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
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
loadGeneExpressionSet   Set of functions to load splicing
                        quantification
loadGtexData            Load GTEx data
loadGtexDataShiny       Shiny wrapper to load GTEx data
loadGtexFile            Load GTEx file
loadLocalFiles          Load local files
loadRequiredData        Missing information modal template
loadSRAproject          Download and load SRA projects
loadSplicingQuantificationSet
                        Set of functions to load splicing
                        quantification
loadTCGAsampleMetadata
                        Prepare TCGA sample metadata from loaded
                        datasets
loadedDataModal         Create a modal warning the user of already
                        loaded data
matchGroupPatientsAndSamples
                        Match patients and samples in a group
matchSplicingEventsWithGenes
                        Match splicing events with respective genes
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
optimSurvDiffSet        Optimal survival difference given an inclusion
                        level cutoff for a specific alternative
                        splicing event
optimalSurvivalCutoff   Calculate optimal data cutoff that best
                        separates survival curves
parseCategoricalGroups
                        Parse categorical columns in a data frame
parseDateResponse       Parse the date from a response
parseFirebrowseMetadata
                        Query the Firebrowse web API for metadata
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 sample information from TCGA samples
parseUniprotXML         Parse XML from UniProt's RESTful service
parseUrlsFromFirebrowseResponse
                        Retrieve URLs from a response to a Firebrowse
                        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
patientMultiMatchWarning
                        Helper text to explain what happens when a
                        patient matches multiple samples when
                        performing survival analysis
performICA              Perform independent component analysis after
                        processing missing values
performPCA              Perform principal component analysis after
                        processing missing values
plotClusters            Add clusters to 'highchart' object
plotCorrelation         Plot correlations
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
plotTranscripts         Plot transcripts
plotVariance            Create the explained variance plot
plottableXranges        HTML code to plot a X-ranges series
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
prepareSRAmetadata      Prepare files to be loaded into psichomics
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
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
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
queryPubMed             Query the PubMed REST API
queryUniprot            Query the UniProt REST API
readAnnot               Read custom or remote annotation
readFile                Load local file
reduceDimensionality    Reduce dimensionality after processing missing
                        values from data frame
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
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
selectGroupsUI          Group selection
selectizeGeneInput      Create input to select a gene
setASevent              Get or set globally accessible elements
setFirebrowseData       Set data from Firebrowse
setLocalData            Load local files
setOperation            Perform set operations on selected groups
setOperationIcon        Create an icon based on set operations
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
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
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
wilcox                  Perform Wilcoxon analysis and return interface
                        to show the results
