[.GEandAScorrelation    Subset correlation results between gene
                        expression and splicing quantification
calculateLoadingsContribution
                        Calculate the contribution of PCA loadings to
                        the selected principal components
colSums,EList-method    Sum columns using an 'EList-class' object
convertGeneIdentifiers
                        Convert gene identifiers
correlateGEandAS        Correlate gene expression data against
                        alternative splicing quantification
createGroupByColumn     Split elements into groups based on a given
                        column of a dataset
diffAnalyses            Perform statistical analyses
ensemblToUniprot        Convert an Ensembl identifier to the respective
                        UniProt identifier
filterGeneExpr          Filter genes based on their expression
filterGroups            Filter groups with less data points than the
                        threshold
filterPSI               Filter alternative splicing quantification
getAttributesTime       Retrieve the time for given columns in a
                        clinical dataset
getDownloadsFolder      Get the Downloads folder of the user
getFirebrowseDataTypes
                        Get data types available from Firebrowse
getFirebrowseDates      Query the Firebrowse web API
getGeneList             Get pre-created, literature-based gene list
getGtexTissues          Get GTEx tissues from given GTEx sample
                        attributes
getMatchingSamples      Get samples matching the given patients
getPatientFromSample    Get patients from given samples
getSplicingEventFromGenes
                        Get alternative splicing events from genes or
                        vice-versa
getSplicingEventTypes   Splicing event types available
getValuePerPatient      Assign average sample values to their
                        corresponding patients
groupByAttribute        Data grouping interface
groupPerElem            Assign one group to each element
isFirebrowseUp          Check whether the Firebrowse web API is running
labelBasedOnCutoff      Label groups based on a given cutoff
listSplicingAnnotations
                        List the alternative splicing annotation files
                        available
loadAnnotation          Load alternative splicing annotation from
                        'AnnotationHub'
loadFirebrowseData      Downloads and processes data from the
                        Firebrowse web API and loads it into R
loadGtexData            Load GTEx data
loadLocalFiles          Load local files
loadSRAproject          Download and load SRA projects
normaliseGeneExpression
                        Filter and normalise gene expression
optimalSurvivalCutoff   Calculate optimal data cutoff that best
                        separates survival curves
parseCategoricalGroups
                        Parse categorical columns in a data frame
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
parseTcgaSampleInfo     Parse sample information from TCGA samples
performICA              Perform independent component analysis after
                        processing missing values
performPCA              Perform principal component analysis after
                        processing missing values
plot.GEandAScorrelation
                        Display results of correlation analyses
plotDistribution        Plot distribution through a density plot
plotGeneExprPerSample   Plot distribution of gene expression per sample
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
plotProtein             Plot protein features
plotRowStats            Plot sample statistics per row
plotSurvivalCurves      Plot survival curves
plotSurvivalPvaluesByCutoff
                        Plot p-values of survival difference between
                        groups based on multiple cutoffs
plotTranscripts         Plot transcripts
plotVariance            Create the explained variance plot from a PCA
prepareAnnotationFromEvents
                        Prepare annotation from alternative splicing
                        events
prepareJunctionQuantSTAR
                        Prepare files to be loaded into psichomics
prepareSRAmetadata      Prepare files to be loaded into psichomics
processSurvTerms        Process survival curves terms to calculate
                        survival curves
psichomics              Start graphical interface of psichomics
quantifySplicing        Quantify alternative splicing events
queryEnsemblByGene      Query information from Ensembl
readFile                Load local file
rowMeans                Calculate mean or variance for each row of a
                        matrix
survdiff.survTerms      Test differences between survival curves
survfit.survTerms       Compute estimates of survival curves
testGroupIndependence   Multiple independence tests between reference
                        groups and list of groups
testSurvival            Test the survival difference between groups of
                        patients
