![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| as.table.GEandAScorrelation | Display results of correlation analyses |
| assignValuePerPatient | Assign average sample values to their corresponding patients |
| assignValuePerSubject | Assign average sample values to their corresponding patients |
| calculateLoadingsContribution | Calculate the contribution of PCA loadings to the selected principal components |
| colSums-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 |
| 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 |
| getColumnsTime | Retrieve the time for given columns in a clinical dataset |
| getDownloadsFolder | Get the Downloads folder of the user |
| getFirebrowseCohorts | Query the Firebrowse web API |
| getFirebrowseDataTypes | Get data types available from Firebrowse |
| getFirebrowseDates | Query the Firebrowse web API |
| getFirehoseDataTypes | Get data types available from Firebrowse |
| getGeneList | Get pre-created, literature-based gene list |
| getGenesFromSplicingEvents | Get alternative splicing events from genes or vice-versa |
| getGtexTissues | Get GTEx tissues from given GTEx sample attributes |
| getMatchingSamples | Get samples matching the given patients |
| getPatientFromSample | Get patients from given samples |
| getPSIperPatient | Assign average sample values to their corresponding patients |
| getSampleFromPatient | Get samples matching the given patients |
| getSampleFromSubject | Get samples matching the given patients |
| getSplicingEventFromGenes | Get alternative splicing events from genes or vice-versa |
| getSplicingEventTypes | Splicing event types available |
| getSubjectFromSample | Get patients from given samples |
| getValuePerPatient | Assign average sample values to their corresponding patients |
| getValuePerSubject | Assign average sample values to their corresponding patients |
| groupByAttribute | Data grouping interface |
| groupByExpression | Data grouping interface |
| groupByGrep | Data grouping interface |
| groupById | Data grouping interface |
| groupByPreMadeList | Data grouping interface |
| groupPerElem | Assign one group to each element |
| groupPerPatient | Assign one group to each element |
| groupPerSample | 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 |
| optimalPSIcutoff | Calculate optimal data cutoff that best separates survival curves |
| optimalSurvivalCutoff | Calculate optimal data cutoff that best separates survival curves |
| parseCategoricalGroups | Parse categorical columns in a data frame |
| parseMatsAnnotation | Get events from alternative splicing annotation |
| parseMisoAnnotation | Get events from alternative splicing annotation |
| 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 |
| parseTcgaSampleInfo | Parse sample information from TCGA samples |
| parseVastToolsAnnotation | Get events from alternative splicing annotation |
| 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 |
| plotCorrelation | 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 |
| 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 |
| print.GEandAScorrelation | Display results of correlation analyses |
| processSurvTerms | Process survival curves terms to calculate survival curves |
| psichomics | Start graphical interface of psichomics |
| quantifySplicing | Quantify alternative splicing events |
| queryEnsemblByEvent | Query information from Ensembl |
| queryEnsemblByGene | Query information from Ensembl |
| readFile | Load local file |
| rowMeans | Calculate mean or variance for each row of a matrix |
| rowVars | 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 patients |
| [.GEandAScorrelation | Subset correlation results between gene expression and splicing quantification |