Man pages for psichomics
Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

addObjectAttrsSet attributes to an object
addTCGAdataCreates a UI set with options to add data from...
analysesTableSetSet of functions to render differential analyses (plot and...
appendNewGroupsAppend new groups to already existing groups
appServerServer logic
appUIUser interface
areSplicingEventsCheck if string identifies splicing events
articleUIReturn the interface to display an article
ASquantFileInputFile input for alternative splicing quantification
assignColoursAssign colours to groups
assignValuePerSubjectAssign average sample values to their corresponding subjects
basicStatsBasic statistics performed on data
blendColoursBlend two HEX colours
browserHistoryEnable history navigation
calculateInclusionLevelsCalculate inclusion levels using alternative splicing event...
calculateLoadingsContributionCalculate the contribution of PCA loadings to the selected...
checkFileFormatChecks the format of a file
checkFirebrowseReturn an user interface depending on the status of the...
checkGroupTypeCheck type of groups within file
checkIntegrityCompute the 32-byte 'MD5' hashes of one or more files and...
checkSurvivalInputPrepare survival terms in case of valid input
clusterICAsetServer logic for clustering ICA data
clusterSetServer logic for clustering PCA data
colourInputModModified colour input with 100% width
colSums-EList-methodSum columns using an 'EList-class' object
convertGeneIdentifiersConvert gene identifiers
correlateGEandASCorrelate gene expression data against alternative splicing...
createDataTabRender a specific data tab (including data table and related...
createDensitySparklinesCreate density sparklines for inclusion levels
createEventPlottingCreate plot for events
createGroupPrepare to create group according to specific details
createGroupByAttributeSplit elements into groups based on a given column of a...
createGroupByIdCreate groups based on given row indexes or identifiers
createGroupFromInputSet new groups according to the user input
createJunctionsTemplateCreates a template of alternative splicing junctions
createOptimalSurvDataCreate survival data based on a PSI cutoff
createSparklinesCreate sparkline charts to be used in a data table
customRowMeansCalculate statistics for each row or column of a matrix
diagramSplicingEventPrepare SVG diagram of alternative splicing events
diffAnalysesPerform statistical analyses
diffExpressionSetSet of functions to perform differential analyses
diffSplicingSetSet of functions to perform differential analyses
disableTabEnable or disable a tab from the 'navbar'
discardLowCoveragePSIvaluesRemove alternative splicing quantification values based on...
discardOutsideSamplesFromGroupsDiscard grouped samples if not within a sample vector
displayDisplay characters in the command-line
dot-onAttachPrint startup message
downloadFilesDownload files to a given directory
ensemblToUniprotConvert from Ensembl to UniProt identifier
escapeEscape symbols for use in regular expressions
eventPlotOptionsOptions for event plotting
exportGroupsToFileExport groups to a file
export_highchartsAdd an exporting feature to a 'highcharts' object
fileBrowserInteractive folder selection using a native dialogue
fileBrowserInputFile browser input
filterGeneExprFilter genes based on their expression
filterGroupsFilter groups with less data points than the threshold
filterPSIFilter alternative splicing quantification
findASeventsFromGeneFind splicing events based on given genes
findEventDataLook for event data in input
geneExprFileInputFile input for gene expression
geneExprSurvSetLogic set to perform survival analysis based on gene...
geNormalisationFilteringInterfaceInterface to normalise and filter gene expression
getAttributesTimeGet time values for given columns in a clinical dataset
getClinicalDataForSurvivalRetrieve clinical data based on attributes required for...
getClinicalMatchFromGet or set clinical matches from a given data type
getDataGet global data
getDataRowsGet rows of a data frame between two row indexes
getDifferentialExpressionGet or set differential expression' elements for a data...
getDifferentialSplicingGet or set differential splicing' elements for a data...
getDownloadsFolderGet the path to the Downloads folder
getFirebrowseDateFormatReturns the date format used by the Firebrowse API
getGeneListGet curated, literature-based gene lists
getGlobalGet or set globally accessible elements
getGroupsGet or set groups
getGtexDataTypesGet GTEx data information
getGtexDataURLGet links to download GTEx data
getGtexTissuesGet GTEx tissues from given GTEx sample attributes
getHiddenGet or set hidden globally accessible elements
getHighlightedPointsGet or set points or regions for plots
getNumericsConvert a column to numeric if possible and ignore given...
getSampleFromSubjectGet samples matching the given subjects
getServerFunctionsMatches server functions from a given loader
getSplicingEventCoordinatesReturns the coordinates of interest for a given event type
getSplicingEventDataGet splicing event information for given alternative splicing...
getSplicingEventFromGenesGet alternative splicing events from genes or vice-versa
getSplicingEventTypesGet supported splicing event types
getSubjectFromSampleGet subjects from given samples
getTCGAdataTypesGet available parameters for TCGA data
getUiFunctionsMatches user interface (UI) functions from a given loader
getValidEventsFilters the events with valid elements according to the given...
ggplotServerLogic set to create an interactive 'ggplot'
ggplotTooltipCreate the interface for the tooltip of a plot
ggplotUIInterface for interactive 'ggplot'
globalSelectizeCreate a 'selectize' input available from any page
groupByAttributeData grouping interface
groupManipulationLogic server to manipulate data grouping
groupManipulationInputInterface to manipulate data grouping
groupPerElemAssign one group to each element
groupsServerOnceServer function for data grouping (one call)
hchart.survfitPlot survival curves
hc_scatterCreate scatter plot
HTMLfastFaster version of 'shiny::HTML'
importGroupsFromImport groups from a file
inclusionLevelsFilterInterfaceInterface to filter alternative splicing
inclusionLevelsInterfaceInterface to quantify alternative splicing
inlineDialogAlert in the style of a dialogue box with a button
insideFileGet psichomics file inside a given directory
isFileCheck if files exist
isFirebrowseUpCheck if Firebrowse API is running
isRStudioServerCheck if running in RStudio Server
is.wholeCheck if a number is whole
joinEventsPerTypeFull outer join all given events based on select columns
junctionStringString used to search for matches in a junction...
labelBasedOnCutoffLabel groups based on a given cutoff
leveneTestLevene's test
linkToArticlespsichomics article's link interface
linkToRunJSLink to run arbitrary JavaScript code
listAllAnnotationsList alternative splicing annotation files available, as well...
listSplicingAnnotationsList alternative splicing annotations
loadAnnotationLoad alternative splicing annotation from 'AnnotationHub'
loadByCheck if a given function should be loaded by the calling...
loadCustomSplicingAnnotationSetSet of functions to load a custom alternative splicing...
loadedDataModalWarn user about loaded data
loadFileLoad file based on its format
loadFileFormatsLoad supported file formats
loadFirebrowseFoldersLoad Firebrowse folders
loadGeneExpressionSetSet of functions to load splicing quantification
loadGtexDataDownload and load GTEx data
loadGtexDataShinyShiny wrapper to load GTEx data
loadGtexFileLoad GTEx file
loadLocalFilesLoad local files
loadSplicingQuantificationSetSet of functions to load splicing quantification
loadSRAprojectDownload and load SRA projects via recount2
loadTCGAdataDownload and process TCGA data
loadTCGAsampleMetadataPrepare TCGA sample metadata from loaded datasets
matchGroupASeventsAndGenesMatch AS events and genes in a group
matchGroupSubjectsAndSamplesMatch subjects and samples in a group
matchSplicingEventsWithGenesMatch splicing events with respective genes
missingDataModalMissing information modal template
modTabPanelModified 'tabPanel' function to show icon and title
navSelectizeCreate a special 'selectize' input in the navigation bar
normaliseGeneExpressionFilter and normalise gene expression
operateOnGroupsSet operations on groups
optimalSurvivalCutoffCalculate optimal data cutoff that best separates survival...
optimSurvDiffSetOptimal survival difference given an inclusion level cutoff...
parseCategoricalGroupsParse categorical columns in a data frame
parseDateResponseParse the date from a response
parseFileParse file according to its format
parseFirebrowseMetadataQuery the Firebrowse API for metadata
parseMatsEventParse alternative splicing events from MATS
parseMatsGenericParse junctions of an alternative splicing event from MATS...
parseMisoAnnotationParse events from alternative splicing annotation
parseMisoEventParse an alternative splicing event from MISO
parseMisoEventIDMatch MISO's splicing event IDs with the IDs present in the...
parseMisoGenericParse junctions of an event from MISO according to event type
parseMisoIdParse MISO's alternative splicing event identifier
parseSplicingEventParse alternative splicing event identifier
parseSuppaEventParses splicing events of a specific event type from SUPPA
parseSuppaGenericParse junctions of an event from SUPPA
parseTcgaSampleInfoParse sample information from TCGA sample identifiers
parseUniprotXMLParse XML from UniProt REST service
parseUrlsFromFirebrowseResponseRetrieve URLs from a response to a Firebrowse data query
parseVastToolsEventParses an alternative splicing event from VAST-TOOLS
parseVastToolsSEParse junctions of an event from VAST-TOOLS according to...
performICAPerform independent component analysis after processing...
performPCAPerform principal component analysis after processing missing...
plotClustersAdd clusters to 'highchart' object
plotDistributionPlot distribution using a density plot
plot.GEandAScorrelationDisplay results of correlation analyses
plotGeneExprPerSamplePlot distribution of gene expression per sample
plotGroupIndependencePlot '-log10(p-values)' of the results obtained after...
plotICACreate multiple scatterplots from ICA
plotLibrarySizePlot library size
plotPCACreate a scatterplot from a PCA object
plotPCAvarianceCreate the explained variance plot from a PCA
plotPointsStyleInterface to modify the style of the plot points
plotProteinPlot protein features
plotRowStatsPlot row-wise statistics
plotSingleICACreate a scatterplot for ICA
plotSplicingEventPlot diagram of alternative splicing events
plotSurvivalCurvesPlot survival curves
plotSurvivalPvaluesByCutoffPlot p-values of survival difference between groups based on...
plottableXrangesHTML code to plot a X-ranges series
plotTranscriptsPlot transcripts
prepareAnnotationFromEventsPrepare annotation from alternative splicing events
prepareEventPlotOptionsPrepare event plot options
prepareFileBrowserPrepare file browser dialogue and update the input's value...
prepareFirebrowseArchivesPrepares Firebrowse archives in a given directory
prepareGenePresentationPrepare presentation of multiple genes for the same splicing...
prepareJunctionQuantSTARPrepare user-provided files to be loaded into psichomics
preparePreMadeGroupForSelectionPrepare list of pre-made groups for a 'selectize' element
prepareSRAmetadataPrepare user-provided files to be loaded into psichomics
prepareWordBreakCreate word break opportunities (for HTML) using given...
preserveAttributesPreserve attributes when extracting values
processButtonStyle button used to initiate a process
processDatasetNamesProcess dataset names
processSRAdataProcess SRA quantification data
processSurvDataProcess survival data to calculate survival curves
processSurvivalCheck if survival analyses successfully completed or returned...
processSurvTermsProcess survival curves terms to calculate survival curves
psichomicsStart graphical interface of psichomics
pubmedUIReturn the interface of relevant PubMed articles for a given...
quantifySplicingQuantify alternative splicing events
quantifySplicingSetSet of functions to quantify alternative splicing
queryEnsemblQuery the Ensembl REST API
queryEnsemblByGeneQuery information from Ensembl
queryFirebrowseDataQuery the Firebrowse API for TCGA data
queryPubMedQuery the PubMed REST API
queryUniprotQuery the UniProt REST API
readAnnotRead custom or remote annotation
readFileLoad psichomics-specific file
reduceDimensionalityReduce dimensionality after processing missing values from...
renameDuplicatedRename vector to avoid duplicated values with another vector
renameGroupsRename duplicated names from a new group
renderBoxplotRender boxplot
renderDataTableSparklinesRender a data table with sparkline HTML elements
renderGeneticInfoRender genetic information
renderGroupInterfaceRender group interface
renderProteinInfoRender protein information
rm.nullFilter 'NULL' elements from a vector or a list
roundDigitsRound by the given number of digits
roundMinDownRound down/up the minimum/maximum value
saveProcessedSRAdataSave processed SRA data in file
selectGroupsUIGroup selection
selectizeGeneInputCreate input to select a gene
selectPreMadeGroupSelect pre-made groups from a selected item
setFirebrowseDataSet data from Firebrowse
setLocalDataLoad local files
setOperationPerform set operations on selected groups
setOperationIconCreate an icon based on set operations
showAlertShow or remove an alert
showGroupsTablePresent groups table
sidebarSidebar without a well
signifDigitsGet number of significant digits
singleDiffAnalysesPerform statistical analysis on a given splicing event
sortCoordinatesSort coordinates for some event types
startProcessSet the status of a process to style a given button
startProgressCreate, set and terminate a progress object
styleModalCreate a modal window
subjectMultiMatchWarningHelper text to explain what happens when a subject matches...
subsetGeneExpressionFromMatchingGenesSubset gene expression based on (full or partial) matching...
survdiffTermsTest Survival Curve Differences
survfit.survTermsCreate survival curves
tabDatasetCreates a 'tabPanel' template for a 'datatable' with a title...
table2htmlCreate HTML table from data frame or matrix
tableRowCreate a row for a HTML table
testGroupIndependenceMultiple independence tests between reference groups and list...
testSingleIndependenceMultiple independence tests between a reference group and...
testSurvivalTest the survival difference between groups of subjects
testSurvivalCutoffTest the survival difference between two survival groups...
textSuggestionsCreate script for auto-completion of text input
toJSarrayConvert vector of values to JavaScript array
transformDataTransform data in data frame
transformOptionsShow variable transformation(s)
transformValuesTransform values as per a given type of transformation
trimWhitespaceTrims whitespace from a word
t.stickyPreserve attributes of 'sticky' objects when extracting or...
uniqueByCheck unique rows of a data frame based on a set of its...
updateClinicalParamsUpdate available clinical attributes when the clinical data...
updateFileBrowserInputChange the value of a 'fileBrowserInput()' on the client
vennEventsCompare the number of events from the different programs in a...
wilcoxPerform and display statistical analysis
psichomics documentation built on Nov. 8, 2020, 5:44 p.m.