[.GEandAScorrelation    Display results of correlation analyses
assignValuePerSubject   Assign average sample values to their
                        corresponding subjects
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
createGroupByAttribute
                        Split elements into groups based on a given
                        column of a dataset
diffAnalyses            Perform statistical analyses
ensemblToUniprot        Convert from Ensembl to 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       Get time values for given columns in a clinical
                        dataset
getDownloadsFolder      Get the path to the Downloads folder
getGeneList             Get curated, literature-based gene lists
getGtexDataTypes        Get GTEx data types
getGtexTissues          Get GTEx tissues from given GTEx sample
                        attributes
getMatchingSamples      Get samples matching the given subjects
getSplicingEventFromGenes
                        Get alternative splicing events from genes or
                        vice-versa
getSplicingEventTypes   Get supported splicing event types
getSubjectFromSample    Get subjects from given samples
getTCGAdataTypes        Get available parameters for TCGA data
groupPerElem            Assign one group to each element
isFirebrowseUp          Check if Firebrowse API is running
labelBasedOnCutoff      Label groups based on a given cutoff
listSplicingAnnotations
                        List alternative splicing annotations
loadAnnotation          Load alternative splicing annotation from
                        'AnnotationHub'
loadGtexData            Load GTEx data
loadLocalFiles          Load local files
loadSRAproject          Download and load SRA projects via recount2
loadTCGAdata            Download and process TCGA data
normaliseGeneExpression
                        Filter and normalise gene expression
optimalSurvivalCutoff   Calculate optimal data cutoff that best
                        separates survival curves
parseCategoricalGroups
                        Parse categorical columns in a data frame
parseSplicingEvent      Parse alternative splicing event identifier
parseSuppaAnnotation    Get events from alternative splicing annotation
parseTCGAsampleTypes    Parse sample information from TCGA sample
                        identifiers
performICA              Perform independent component analysis after
                        processing missing values
performPCA              Perform principal component analysis after
                        processing missing values
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
plotSplicingEvent       Plot diagram of alternative splicing events
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
prepareSRAmetadata      Prepare user-provided 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 psichomics-specific file
rowMeans                Calculate mean or variance for each row of a
                        matrix
survdiffTerms           Test Survival Curve Differences
survfit.survTerms       Create survival curves
testGroupIndependence   Multiple independence tests between reference
                        groups and list of groups
testSurvival            Test the survival difference between groups of
                        subjects
