psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation
Version 1.2.1

Interactive R package with a Shiny-based graphical interface for the quantification, analysis and visualisation of alternative splicing data from The Cancer Genome Atlas (TCGA) or the Genotype-Tissue Expression (GTEx) project. This tool interactively performs survival, principal components and differential splicing analyses with direct incorporation of clinical features (such as tumour stage or survival) associated with TCGA and GTEx samples.

Browse man pages Browse package API and functions Browse package files

AuthorNuno Saraiva-Agostinho [aut, cre], Nuno Barbosa-Morais [aut, led, ths], André Falcão [ths], Lina Gallego Paez [ctb], Marie Bordone [ctb], Teresa Maia [ctb], Mariana Ferreira [ctb], Ana Carolina Leote [ctb], Bernardo Almeida [ctb]
Bioconductor views AlternativeSplicing BiomedicalInformatics DifferentialSplicing GUI MultipleComparison PrincipalComponent RNASeq Sequencing Survival Transcription Transcriptomics Visualization
Date of publicationNone
MaintainerNuno Saraiva-Agostinho <nunodanielagostinho@gmail.com>
LicenseMIT + file LICENSE
Version1.2.1
URL https://github.com/nuno-agostinho/psichomics
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("psichomics")

Man pages

addTCGAdata: Creates a UI set with options to add data from...
analysesServer: Server logic for the analyses
analysesUI: User interface for the data analyses
appServer: Server function
appUI: The user interface (ui) controls the layout and appearance of...
articleUI: Return the interface to display an article
basicStats: Basic statistics performed on data
browserHistory: Enable history navigation
bsModal2: Modified version of shinyBS::bsModal
calculateInclusionLevels: Calculate inclusion levels using alternative splicing event...
checkFileFormat: Checks the format of a file
checkFirebrowse: Return an user interface depending on the status of the...
checkIntegrity: Compute the 32-byte MD5 hashes of one or more files and check...
checkSurvivalInput: Prepare survival terms in case of valid input
closeProgress: Close the progress even if there's an error
createDataTab: Render a specific data tab (including data table and related...
createDensitySparklines: Create density sparklines for inclusion levels
createEventPlotting: Create plot for events
createGroup: Prepare to create group according to specific details
createGroupByAttribute: Create groups with the indexes from the unique values of a...
createGroupByColumn: Create groups with the indexes from the unique values of a...
createGroupById: Create groups from a given string of rows
createGroupFromInput: Set new groups according to the user input
createJunctionsTemplate: Creates a template of alternative splicing junctions
createTooltip: Create the interface for the tooltip of a plot
dataServer: Server logic of the data module
dataUI: User interface of the data module
diffAnalyses: Perform selected statistical analyses on multiple splicing...
diffSplicingEventServer: Server logic for the analyses of a single alternative...
diffSplicingEventUI: Interface for the analysis of an alternative splicing event
diffSplicingServer: Server logic for the differential splicing analyses
diffSplicingTableServer: Server logic of the exploratory differential analyses
diffSplicingTableUI: Interface for differential analyses on all splicing events
diffSplicingUI: User interface for the differential splicing analyses
disableTab: Disable a tab from the navbar
downloadFiles: Download files to a given directory
echoProgress: Echo progress to console using 'cat'
enableTab: Enable a tab from the navbar
endProcess: Signal the program that a process has ended
ensemblToUniprot: Convert a protein's Ensembl identifier to UniProt identifier
errorDialog: Error alert in the style of a dialog box with a button
escape: Escape symbols for use in regular expressions
eventPlotOptions: Options for event plotting
export_highcharts: Add an exporting feature to a 'highcharts' object
filterGroups: Filter groups with less data points than the threshold
firebrowseUI: User interface of the TCGA/Firebrowse loader
fisher: Perform Fisher's exact test and return interface to show the...
fligner: Perform Fligner-Killeen test and return interface to show the...
getActiveDataset: Get selected dataset
getAssemblyVersion: Get the assembly version of a data category
getAutoNavigation: Get if history browsing is automatic
getCategories: Get available data categories
getCategory: Get selected data category
getCategoryData: Get data of selected data category
getClinicalData: Get clinical data of the data category
getClinicalMatchFrom: Get clinical matches from a given data type
getColumnsTime: Retrieve the time for given columns in a clinical dataset
getCores: Get number of cores to use
getData: Get global data
getDataRows: Get rows of a data frame between two row indexes
getDifferentialAnalyses: Get the table of differential analyses of a data category
getDifferentialAnalysesFiltered: Get the filtered table of differential analyses of a data...
getDifferentialAnalysesHighlightedEvents: Get highlighted events from differential analyses of a data...
getDifferentialAnalysesSelected: Get selected points in the differential analysis table of a...
getDifferentialAnalysesSurvival: Get the table of differential analyses' survival data of a...
getDifferentialAnalysesZoom: Get plot coordinates for zooming from differential analyses...
getDownloadsFolder: Get the Downloads folder of the user
getEvent: Get selected alternative splicing event's identifer
getFirebrowseCohorts: Query the Firebrowse web API for the cohorts available
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 datestamps of the data...
getGlobal: Get data from global data
getGroupsFrom: Get groups from a given data type
getInclusionLevels: Get alternative splicing quantification of the selected data...
getInclusionLevelsPCA: Get principal component analysis based on inclusion levels
getJunctionQuantification: Get junction quantification data
getMatchingSamples: Search samples in the clinical dataset and return the ones...
getNumerics: Convert a column to numeric if possible and ignore given...
getPatientFromSample: Match given sample identifiers and return the respective row...
getPatientId: Get the identifier of patients for a given category
getPrecision: Get number of decimal places
getPSIperPatient: Assign alternative splicing quantification to patients based...
getSampleId: Get the identifier of samples for a given category
getSampleInfo: Get sample information of the selected data category
getSelectedGroups: Get selected groups for a given group selection element
getServerFunctions: Matches server functions from a given loader
getSignificant: Get number of significant digits
getSpecies: Get the species of a data category
getSplicingEventCoordinates: Returns the coordinates of interest for a given event type
getSplicingEventTypes: Splicing event types available
getUiFunctions: Matches user interface (UI) functions from a given loader
getURLtoDownload: Get the URL links to download
getValidEvents: Filters the events with valid elements according to the given...
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
groupPerPatient: Assign one group to each patient
groupPerSample: Assign one group to each sample
groupsServer: Server function for data grouping
groupsServerOnce: Server function for data grouping (one call)
groupsUI: Creates UI elements for the grouping feature
gtexDataServer: Server logic to load GTEx data
gtexDataUI: Interface to load GTEx data
hchart.survfit: Plot survival curves using Highcharts
hc_scatter: Create scatter plot
helpServer: Server logic of the help menu
helpUI: User interface of the help menu
inclusionLevelsInterface: Interface to quantify alternative splicing
inclusionLevelsServer: Server logic of the alternative splicing event quantification...
inclusionLevelsUI: Interface of the alternative splicing event quantification...
infoServer: Server logic
infoUI: Information's user interface
insideFile: Get psichomics file inside a given directory
isFirebrowseUp: Check if the Firebrowse web API is running
is.whole: Check if a number is whole
joinEventsPerType: Full outer join all given events based on select columns
junctionString: String used to search for matches in a junction...
kruskal: Perform Kruskal's test and return interface to show the...
labelBasedOnCutoff: Label groups based on a given cut-off
levene: Perform Levene's test and return interface to show the...
leveneTest: Levene's test
listAllAnnotations: List alternative splicing annotation files available, as well...
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...
loadedDataModal: Create a modal warning the user of already loaded data
loadFile: Loads a file according to its format
loadFileFormats: Loads file formats
loadFirebrowseData: Downloads and processes data from the Firebrowse web API and...
loadFirebrowseFolders: Load Firebrowse folders
loadGtexData: Load GTEx data given input
loadLocalFiles: Load local files
localDataServer: Server logic to load local data
localDataUI: Interface to load local data
missingDataModal: Missing information modal template
modTabPanel: Modified tabPanel function to show icon and title
navSelectize: Create a special selectize input in the navigatin bar
noinfo: Interface when no information could be retrieved
operateOnGroups: Set operations on groups
optimalPSIcutoff: Calculate optimal alternative splicing quantification cut-off...
optimSurvDiff: Optimal survival difference given an inclusion level cut-off...
parseDateResponse: Parse the date from a response
parseFirebrowseMetadata: Query the Firebrowse web API for metadata and parse the...
parseMatsEvent: Parse alternative splicing events from MATS
parseMatsGeneric: Parse junctions of an alternative splicing event from MATS...
parseMisoAnnotation: Get events from alternative splicing annotation
parseMisoEvent: Parse an alternative splicing event from MISO
parseMisoEventID: Match MISO's splicing event IDs with the IDs present in the...
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...
parseSuppaEvent: Parses splicing events of a specific event type from SUPPA
parseSuppaGeneric: Parse junctions of an event from SUPPA
parseTcgaSampleInfo: Parse and prepare 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...
pcaServer: Server logic for the principal component analysis
pcaUI: User interface of the principal component analysis
performPCA: Perform principal component analysis after processing missing...
plotDistribution: Plot distribution through a density plot
plotMiniSurvivalCurves: Perform and plot survival curves
plotPCA: Create a scatterplot from a PCA object
plotPointsStyle: Interface to modify the style of the plot points
plotProtein: Plot protein features
plotSurvivalCurves: Plot survival curves
plottableXranges: HTML code to plot a X-ranges series
plotTranscripts: Plot transcripts
plotVariance: Create the explained variance plot
prepareAnnotationFromEvents: Prepare annotation from alternative splicing events
prepareFirebrowseArchives: Prepares Firebrowse archives in a given directory
processButton: Style button used to initiate a process
processDatasetNames: Process dataset names
processSurvData: Process survival data to calculate survival curves
processSurvival: Check if survival analyses successfully completed or returned...
processSurvTerms: Process survival curves terms to calculate survival curves
psichomics: Start graphical interface of PSICHOMICS
pubmedUI: Return the interface of relevant PubMed articles for a given...
quantifySplicing: Quantify alternative splicing events
queryEnsembl: Query the Ensembl REST API
queryEnsemblByEvent: Query information from Ensembl by a given alternative...
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
readFile: Load local file
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
renderProteinInfo: Render protein information
rm.null: Filter NULL elements from vector or list
roundDigits: Round by the given number of digits
rowVar: Sample variance by row
selectGroupsServer: Group selection logic
selectGroupsUI: Group selection interface
setActiveDataset: Set active dataset
setAssemblyVersion: Set the assembly version of a data category
setAutoNavigation: Set if history browsing is automatic
setCategory: Set data category
setClinicalMatchFrom: Set clinical matches from a given data type
setCores: Set number of cores
setData: Set data of the global data
setDifferentialAnalyses: Set the table of differential analyses of a data category
setDifferentialAnalysesFiltered: Set the filtered table of differential analyses of a data...
setDifferentialAnalysesHighlightedEvents: Set highlighted events from differential analyses of a data...
setDifferentialAnalysesSelected: Set selected points in the differential analysis table of a...
setDifferentialAnalysesSurvival: Set the table of differential analyses' survival data of a...
setDifferentialAnalysesZoom: Set plot coordinates for zooming from differential analyses...
setEvent: Set event
setFirebrowseData: Set data from Firebrowse
setGlobal: Set element as globally accessible
setGroupsFrom: Set groups from a given data type
setInclusionLevels: Set inclusion levels for a given data category
setInclusionLevelsPCA: Get principal component analysis based on inclusion levels
setLocalData: Load local files
setPatientId: Set the identifier of patients for a data category
setPrecision: Set number of decimal places
setSampleId: Set the identifier of samples for a data category
setSampleInfo: Set sample information for a given data category
setSignificant: Set number of significant digits
setSpecies: Set the species of a data category
setURLtoDownload: Set URL links to download
showAlert: Show or remove an alert
showGroupsTable: Present groups table
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...
startProcess: Signal the program that a process is starting
startProgress: Create a progress object
styleModal: Style and show a modal
survdiff.survTerms: Test difference between two or more survival curves using...
survfit.survTerms: Compute estime of a survival curve using processed survival...
survivalServer: Server logic of survival analysis
survivalUI: User interface of survival analysis
tabDataset: Creates a tabPanel template for a datatable with a title and...
templateServer: Server logic of template
templateUI: User interface of template
testSurvival: Test the survival difference between survival groups
testSurvivalCutoff: Test the survival difference between two survival groups...
textSuggestions: Create script for autocompletion of text input
timePerPatient: Get all columns matching a given string and return a single...
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...
uniqueBy: Check unique rows of a data frame based on a set of its...
updateClinicalParams: Update available clinical attributes when the clinical data...
updateProgress: Update a progress object
vennEvents: Compare the number of events from the different programs in a...
wilcox: Perform Wilcoxon analysis and return interface to show the...

Functions

addTCGAdata Man page Source code
analysesServer Man page Source code
analysesUI Man page Source code
appServer Man page Source code
appUI Man page Source code
articleUI Man page Source code
basicStats Man page Source code
browserHistory Man page Source code
bsModal2 Man page Source code
calculateInclusionLevels Man page Source code
checkFileFormat Man page Source code
checkFirebrowse Man page Source code
checkIntegrity Man page Source code
checkSurvivalInput Man page Source code
closeProgress Man page Source code
colsAsNumbers Source code
createDataTab Man page Source code
createDensitySparklines Man page Source code
createEventPlotting Man page Source code
createGroup Man page Source code
createGroupByAttribute Man page Source code
createGroupByColumn Man page Source code
createGroupById Man page Source code
createGroupFromInput Man page Source code
createJunctionsTemplate Man page Source code
createTooltip Man page Source code
dataServer Man page Source code
dataUI Man page Source code
diffAnalyses Man page Source code
diffSplicingEventServer Man page Source code
diffSplicingEventUI Man page Source code
diffSplicingServer Man page Source code
diffSplicingTableServer Man page Source code
diffSplicingTableUI Man page Source code
diffSplicingUI Man page Source code
disableTab Man page Source code
downloadFiles Man page Source code
echoProgress Man page Source code
enableTab Man page Source code
endProcess Man page Source code
ensemblToUniprot Man page Source code
errorAlert Man page Source code
errorDialog Man page Source code
errorModal Man page Source code
escape Man page Source code
eventPlotOptions Man page Source code
export_highcharts Man page Source code
filterGroups Man page Source code
firebrowseGeneExpressionFormat Source code
firebrowseJunctionReadsFormat Source code
firebrowseMergeClinicalFormat Source code
firebrowseServer Source code
firebrowseUI Man page Source code
fisher Man page Source code
fligner Man page Source code
getActiveDataset Man page
getAssemblyVersion Man page Source code
getAutoNavigation Man page
getCategories Man page
getCategory Man page
getCategoryData Man page
getClinicalData Man page
getClinicalMatchFrom Man page Source code
getColumnsTime Man page Source code
getCores Man page
getData Man page
getDataRows Man page Source code
getDifferentialAnalyses Man page Source code
getDifferentialAnalysesFiltered Man page Source code
getDifferentialAnalysesHighlightedEvents Man page Source code
getDifferentialAnalysesSelected Man page Source code
getDifferentialAnalysesSurvival Man page Source code
getDifferentialAnalysesZoom Man page Source code
getDownloadsFolder Man page Source code
getEvent Man page
getFirebrowseCohorts Man page Source code
getFirebrowseDataTypes Man page Source code
getFirebrowseDateFormat Man page Source code
getFirebrowseDates Man page Source code
getFirehoseCohorts Man page
getFirehoseDataTypes Man page
getFirehoseDates Man page
getGlobal Man page Source code
getGroupsFrom Man page Source code
getInclusionLevels Man page
getInclusionLevelsPCA Man page Source code
getJunctionQuantification Man page Source code
getMatchingSamples Man page Source code
getNumerics Man page Source code
getPSIperPatient Man page Source code
getPatientFromSample Man page Source code
getPatientId Man page Source code
getPrecision Man page
getSampleId Man page Source code
getSampleInfo Man page
getSelectedGroups Man page Source code
getServerFunctions Man page Source code
getSignificant Man page
getSpecies Man page Source code
getSplicingEventCoordinates Man page Source code
getSplicingEventTypes Man page Source code
getURLtoDownload Man page Source code
getUiFunctions Man page Source code
getValidEvents Man page Source code
globalSelectize Man page Source code
groupByAttribute Man page Source code
groupByExpression Man page Source code
groupByGrep Man page Source code
groupById Man page Source code
groupPerPatient Man page Source code
groupPerSample Man page Source code
groupsServer Man page Source code
groupsServerOnce Man page Source code
groupsUI Man page Source code
gtexClinicalInfoFormat Source code
gtexDataServer Man page Source code
gtexDataUI Man page Source code
gtexJunctionReadsFormat Source code
gtexSampleInfoFormat Source code
hc_scatter Man page Source code
hchart.survfit Man page Source code
helpServer Man page Source code
helpUI Man page Source code
inclusionLevelsInterface Man page Source code
inclusionLevelsServer Man page Source code
inclusionLevelsUI Man page Source code
infoModal Man page Source code
infoServer Man page Source code
infoUI Man page Source code
insideFile Man page Source code
is.whole Man page Source code
isFirebrowseUp Man page Source code
isFirehoseUp Man page
joinEventsPerType Man page Source code
junctionString Man page Source code
kruskal Man page Source code
labelBasedOnCutoff Man page Source code
levene Man page Source code
leveneTest Man page Source code
listAllAnnotations Man page Source code
listSplicingAnnotations Man page Source code
loadAnnotation Man page Source code
loadBy Man page Source code
loadFile Man page Source code
loadFileFormats Man page Source code
loadFirebrowseData Man page Source code
loadFirebrowseFolders Man page Source code
loadFirehoseData Man page
loadFirehoseFolders Man page
loadGtexData Man page Source code
loadLocalFiles Man page Source code
loadRequiredData Man page Source code
loadedDataModal Man page Source code
localDataServer Man page Source code
localDataUI Man page Source code
missingDataGuide Man page Source code
missingDataModal Man page Source code
modTabPanel Man page Source code
navSelectize Man page Source code
noinfo Man page Source code
onAttach Source code
operateOnGroups Man page Source code
optimSurvDiff Man page Source code
optimalPSIcutoff Man page Source code
parseDateResponse Man page Source code
parseFirebrowseMetadata Man page Source code
parseFirehoseMetadata Man page
parseMatsA3SS Man page Source code
parseMatsA5SS Man page Source code
parseMatsAFE Man page Source code
parseMatsALE Man page Source code
parseMatsAnnotation Man page Source code
parseMatsEvent Man page Source code
parseMatsGeneric Man page Source code
parseMatsMXE Man page Source code
parseMatsRI Man page Source code
parseMatsSE Man page Source code
parseMisoA3SS Man page Source code
parseMisoA5SS Man page Source code
parseMisoAFE Man page Source code
parseMisoALE Man page Source code
parseMisoAnnotation Man page Source code
parseMisoEvent Man page Source code
parseMisoEventID Man page Source code
parseMisoGeneric Man page Source code
parseMisoId Man page Source code
parseMisoMXE Man page Source code
parseMisoRI Man page Source code
parseMisoSE Man page Source code
parseMisoTandemUTR Man page Source code
parseSampleGroups Man page Source code
parseSplicingEvent Man page Source code
parseSuppaA3SS Man page Source code
parseSuppaA5SS Man page Source code
parseSuppaAFE Man page Source code
parseSuppaALE Man page Source code
parseSuppaAnnotation Man page Source code
parseSuppaEvent Man page Source code
parseSuppaGeneric Man page Source code
parseSuppaMXE Man page Source code
parseSuppaRI Man page Source code
parseSuppaSE Man page Source code
parseTcgaSampleInfo Man page Source code
parseUniprotXML Man page Source code
parseUrlsFromFirebrowseResponse Man page Source code
parseUrlsFromFirehoseResponse Man page
parseValidFile Man page Source code
parseVastToolsA3SS Man page Source code
parseVastToolsA5SS Man page Source code
parseVastToolsAnnotation Man page Source code
parseVastToolsEvent Man page Source code
parseVastToolsRI Man page Source code
parseVastToolsSE Man page Source code
pcaServer Man page Source code
pcaUI Man page Source code
performPCA Man page Source code
plotDistribution Man page Source code
plotMiniSurvivalCurves Man page Source code
plotPCA Man page Source code
plotPointsStyle Man page Source code
plotProtein Man page Source code
plotSurvivalCurves Man page Source code
plotTranscripts Man page Source code
plotVariance Man page Source code
plottableXranges Man page Source code
prepareAnnotationFromEvents Man page Source code
prepareFirebrowseArchives Man page Source code
prepareFirehoseArchives Man page
processButton Man page Source code
processDatasetNames Man page Source code
processSurvData Man page Source code
processSurvTerms Man page Source code
processSurvival Man page Source code
psichomics Man page Source code
pubmedUI Man page Source code
quantifySplicing Man page Source code
queryEnsembl Man page Source code
queryEnsemblByEvent Man page Source code
queryEnsemblByGene Man page Source code
queryFirebrowseData Man page Source code
queryFirehoseData Man page
queryPubMed Man page Source code
queryUniprot Man page Source code
readFile Man page Source code
removeAlert Man page Source code
renameDuplicated Man page Source code
renameGroups Man page Source code
renderDataTableSparklines Man page Source code
renderGeneticInfo Man page Source code
renderProteinInfo Man page Source code
rm.null Man page Source code
roundDigits Man page Source code
rowVar Man page Source code
selectGroupsServer Man page Source code
selectGroupsUI Man page Source code
setActiveDataset Man page Source code
setAssemblyVersion Man page Source code
setAutoNavigation Man page Source code
setCategory Man page Source code
setClinicalMatchFrom Man page Source code
setCores Man page Source code
setData Man page Source code
setDifferentialAnalyses Man page Source code
setDifferentialAnalysesFiltered Man page Source code
setDifferentialAnalysesHighlightedEvents Man page Source code
setDifferentialAnalysesSelected Man page Source code
setDifferentialAnalysesSurvival Man page Source code
setDifferentialAnalysesZoom Man page Source code
setEvent Man page Source code
setFirebrowseData Man page Source code
setGlobal Man page Source code
setGroupsFrom Man page Source code
setInclusionLevels Man page Source code
setInclusionLevelsPCA Man page Source code
setLocalData Man page Source code
setPatientId Man page Source code
setPrecision Man page Source code
setSampleId Man page Source code
setSampleInfo Man page Source code
setSignificant Man page Source code
setSpecies Man page Source code
setURLtoDownload Man page Source code
showAlert Man page Source code
showGroupsTable Man page Source code
signifDigits Man page Source code
singleDiffAnalyses Man page Source code
sortCoordinates Man page Source code
spearman Man page Source code
startProcess Man page Source code
startProgress Man page Source code
styleModal Man page Source code
survdiff.survTerms Man page Source code
survfit.survTerms Man page Source code
survivalServer Man page Source code
survivalUI Man page Source code
tabDataset Man page Source code
templateServer Man page Source code
templateUI Man page Source code
testSurvival Man page Source code
testSurvivalCutoff Man page Source code
textSuggestions Man page Source code
timePerPatient Man page Source code
transformData Man page Source code
transformOptions Man page Source code
transformValues Man page Source code
trimWhitespace Man page Source code
ttest Man page Source code
uniqueBy Man page Source code
updateClinicalParams Man page Source code
updateProgress Man page Source code
vennEvents Man page Source code
warningAlert Man page Source code
warningModal Man page Source code
wilcox Man page Source code

Files

DESCRIPTION
LICENSE
NAMESPACE
NEWS
R
R/analysis.R
R/analysis_diffSplicing.R
R/analysis_diffSplicing_event.R
R/analysis_diffSplicing_table.R
R/analysis_information.R
R/analysis_pca.R
R/analysis_survival.R
R/analysis_template.R
R/app.R
R/data.R
R/data_firebrowse.R
R/data_gtex.R
R/data_inclusionLevels.R
R/data_local.R
R/events.R
R/events_mats.R
R/events_miso.R
R/events_suppa.R
R/events_vastTools.R
R/formats.R
R/formats_firebrowseGeneExpression.R
R/formats_firebrowseJunctionReads.R
R/formats_firebrowseMergeClinical.R
R/formats_gtexClinical.R
R/formats_gtexJunctionReads.R
R/formats_gtexSampleInfo.R
R/globalAccess.R
R/groups.R
R/help.R
R/utils.R
README.md
build
build/vignette.rds
inst
inst/doc
inst/doc/AS_events_preparation.R
inst/doc/AS_events_preparation.Rmd
inst/doc/AS_events_preparation.html
inst/doc/CLI_tutorial.R
inst/doc/CLI_tutorial.Rmd
inst/doc/CLI_tutorial.html
inst/doc/GUI_tutorial.R
inst/doc/GUI_tutorial.Rmd
inst/doc/GUI_tutorial.html
inst/extdata
inst/extdata/TCGAsampleType.RDS
inst/extdata/eventsAnnotSample
inst/extdata/eventsAnnotSample/VASTDB
inst/extdata/eventsAnnotSample/VASTDB/Hsa
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.ALT3.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.ALT5.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.COMBI.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.EXSK.Template.2.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.IR.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MERGE3m.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MIC.Template.txt
inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MULTI.Template.2.txt
inst/extdata/eventsAnnotSample/mats_output
inst/extdata/eventsAnnotSample/mats_output/ASEvents
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.A3SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.A5SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.AFE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.ALE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.MXE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.RI.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.SE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.A3SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.A5SS.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.AFE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.ALE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.MXE.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.RI.txt
inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.SE.txt
inst/extdata/eventsAnnotSample/miso_annotation
inst/extdata/eventsAnnotSample/miso_annotation/A3SS.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/A5SS.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/AFE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/ALE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/MXE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/RI.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/SE.hg19.gff3
inst/extdata/eventsAnnotSample/miso_annotation/TandemUTR.hg19.gff3
inst/extdata/eventsAnnotSample/suppa_output
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_A3.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_A5.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_AF.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_AL.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_MX.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_RI.ioe
inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_SE.ioe
inst/extdata/ex_junctionQuant.RDS
inst/extdata/ex_splicing_annotation.RDS
inst/extdata/miso_AS_annot_example.gff3
inst/shiny
inst/shiny/www
inst/shiny/www/animate.min.css
inst/shiny/www/functions.js
inst/shiny/www/fuzzy.min.js
inst/shiny/www/highcharts.ext.js
inst/shiny/www/jquery.textcomplete.min.js
inst/shiny/www/styles.css
inst/shiny/www/validator.min.js
man
man/addTCGAdata.Rd
man/analysesServer.Rd
man/analysesUI.Rd
man/appServer.Rd
man/appUI.Rd
man/articleUI.Rd
man/basicStats.Rd
man/browserHistory.Rd
man/bsModal2.Rd
man/calculateInclusionLevels.Rd
man/checkFileFormat.Rd
man/checkFirebrowse.Rd
man/checkIntegrity.Rd
man/checkSurvivalInput.Rd
man/closeProgress.Rd
man/createDataTab.Rd
man/createDensitySparklines.Rd
man/createEventPlotting.Rd
man/createGroup.Rd
man/createGroupByAttribute.Rd
man/createGroupByColumn.Rd
man/createGroupById.Rd
man/createGroupFromInput.Rd
man/createJunctionsTemplate.Rd
man/createTooltip.Rd
man/dataServer.Rd
man/dataUI.Rd
man/diffAnalyses.Rd
man/diffSplicingEventServer.Rd
man/diffSplicingEventUI.Rd
man/diffSplicingServer.Rd
man/diffSplicingTableServer.Rd
man/diffSplicingTableUI.Rd
man/diffSplicingUI.Rd
man/disableTab.Rd
man/downloadFiles.Rd
man/echoProgress.Rd
man/enableTab.Rd
man/endProcess.Rd
man/ensemblToUniprot.Rd
man/errorDialog.Rd
man/escape.Rd
man/eventPlotOptions.Rd
man/export_highcharts.Rd
man/filterGroups.Rd
man/firebrowseUI.Rd
man/fisher.Rd
man/fligner.Rd
man/getActiveDataset.Rd
man/getAssemblyVersion.Rd
man/getAutoNavigation.Rd
man/getCategories.Rd
man/getCategory.Rd
man/getCategoryData.Rd
man/getClinicalData.Rd
man/getClinicalMatchFrom.Rd
man/getColumnsTime.Rd
man/getCores.Rd
man/getData.Rd
man/getDataRows.Rd
man/getDifferentialAnalyses.Rd
man/getDifferentialAnalysesFiltered.Rd
man/getDifferentialAnalysesHighlightedEvents.Rd
man/getDifferentialAnalysesSelected.Rd
man/getDifferentialAnalysesSurvival.Rd
man/getDifferentialAnalysesZoom.Rd
man/getDownloadsFolder.Rd
man/getEvent.Rd
man/getFirebrowseCohorts.Rd
man/getFirebrowseDataTypes.Rd
man/getFirebrowseDateFormat.Rd
man/getFirebrowseDates.Rd
man/getGlobal.Rd
man/getGroupsFrom.Rd
man/getInclusionLevels.Rd
man/getInclusionLevelsPCA.Rd
man/getJunctionQuantification.Rd
man/getMatchingSamples.Rd
man/getNumerics.Rd
man/getPSIperPatient.Rd
man/getPatientFromSample.Rd
man/getPatientId.Rd
man/getPrecision.Rd
man/getSampleId.Rd
man/getSampleInfo.Rd
man/getSelectedGroups.Rd
man/getServerFunctions.Rd
man/getSignificant.Rd
man/getSpecies.Rd
man/getSplicingEventCoordinates.Rd
man/getSplicingEventTypes.Rd
man/getURLtoDownload.Rd
man/getUiFunctions.Rd
man/getValidEvents.Rd
man/globalSelectize.Rd
man/groupByAttribute.Rd
man/groupByExpression.Rd
man/groupByGrep.Rd
man/groupById.Rd
man/groupPerPatient.Rd
man/groupPerSample.Rd
man/groupsServer.Rd
man/groupsServerOnce.Rd
man/groupsUI.Rd
man/gtexDataServer.Rd
man/gtexDataUI.Rd
man/hc_scatter.Rd
man/hchart.survfit.Rd
man/helpServer.Rd
man/helpUI.Rd
man/inclusionLevelsInterface.Rd
man/inclusionLevelsServer.Rd
man/inclusionLevelsUI.Rd
man/infoServer.Rd
man/infoUI.Rd
man/insideFile.Rd
man/is.whole.Rd
man/isFirebrowseUp.Rd
man/joinEventsPerType.Rd
man/junctionString.Rd
man/kruskal.Rd
man/labelBasedOnCutoff.Rd
man/levene.Rd
man/leveneTest.Rd
man/listAllAnnotations.Rd
man/listSplicingAnnotations.Rd
man/loadAnnotation.Rd
man/loadBy.Rd
man/loadFile.Rd
man/loadFileFormats.Rd
man/loadFirebrowseData.Rd
man/loadFirebrowseFolders.Rd
man/loadGtexData.Rd
man/loadLocalFiles.Rd
man/loadedDataModal.Rd
man/localDataServer.Rd
man/localDataUI.Rd
man/missingDataModal.Rd
man/modTabPanel.Rd
man/navSelectize.Rd
man/noinfo.Rd
man/operateOnGroups.Rd
man/optimSurvDiff.Rd
man/optimalPSIcutoff.Rd
man/parseDateResponse.Rd
man/parseFirebrowseMetadata.Rd
man/parseMatsEvent.Rd
man/parseMatsGeneric.Rd
man/parseMisoAnnotation.Rd
man/parseMisoEvent.Rd
man/parseMisoEventID.Rd
man/parseMisoGeneric.Rd
man/parseMisoId.Rd
man/parseSampleGroups.Rd
man/parseSplicingEvent.Rd
man/parseSuppaEvent.Rd
man/parseSuppaGeneric.Rd
man/parseTcgaSampleInfo.Rd
man/parseUniprotXML.Rd
man/parseUrlsFromFirebrowseResponse.Rd
man/parseValidFile.Rd
man/parseVastToolsEvent.Rd
man/parseVastToolsSE.Rd
man/pcaServer.Rd
man/pcaUI.Rd
man/performPCA.Rd
man/plotDistribution.Rd
man/plotMiniSurvivalCurves.Rd
man/plotPCA.Rd
man/plotPointsStyle.Rd
man/plotProtein.Rd
man/plotSurvivalCurves.Rd
man/plotTranscripts.Rd
man/plotVariance.Rd
man/plottableXranges.Rd
man/prepareAnnotationFromEvents.Rd
man/prepareFirebrowseArchives.Rd
man/processButton.Rd
man/processDatasetNames.Rd
man/processSurvData.Rd
man/processSurvTerms.Rd
man/processSurvival.Rd
man/psichomics.Rd
man/pubmedUI.Rd
man/quantifySplicing.Rd
man/queryEnsembl.Rd
man/queryEnsemblByEvent.Rd
man/queryEnsemblByGene.Rd
man/queryFirebrowseData.Rd
man/queryPubMed.Rd
man/queryUniprot.Rd
man/readFile.Rd
man/renameDuplicated.Rd
man/renameGroups.Rd
man/renderDataTableSparklines.Rd
man/renderGeneticInfo.Rd
man/renderProteinInfo.Rd
man/rm.null.Rd
man/roundDigits.Rd
man/rowVar.Rd
man/selectGroupsServer.Rd
man/selectGroupsUI.Rd
man/setActiveDataset.Rd
man/setAssemblyVersion.Rd
man/setAutoNavigation.Rd
man/setCategory.Rd
man/setClinicalMatchFrom.Rd
man/setCores.Rd
man/setData.Rd
man/setDifferentialAnalyses.Rd
man/setDifferentialAnalysesFiltered.Rd
man/setDifferentialAnalysesHighlightedEvents.Rd
man/setDifferentialAnalysesSelected.Rd
man/setDifferentialAnalysesSurvival.Rd
man/setDifferentialAnalysesZoom.Rd
man/setEvent.Rd
man/setFirebrowseData.Rd
man/setGlobal.Rd
man/setGroupsFrom.Rd
man/setInclusionLevels.Rd
man/setInclusionLevelsPCA.Rd
man/setLocalData.Rd
man/setPatientId.Rd
man/setPrecision.Rd
man/setSampleId.Rd
man/setSampleInfo.Rd
man/setSignificant.Rd
man/setSpecies.Rd
man/setURLtoDownload.Rd
man/showAlert.Rd
man/showGroupsTable.Rd
man/signifDigits.Rd
man/singleDiffAnalyses.Rd
man/sortCoordinates.Rd
man/spearman.Rd
man/startProcess.Rd
man/startProgress.Rd
man/styleModal.Rd
man/survdiff.survTerms.Rd
man/survfit.survTerms.Rd
man/survivalServer.Rd
man/survivalUI.Rd
man/tabDataset.Rd
man/templateServer.Rd
man/templateUI.Rd
man/testSurvival.Rd
man/testSurvivalCutoff.Rd
man/textSuggestions.Rd
man/timePerPatient.Rd
man/transformData.Rd
man/transformOptions.Rd
man/transformValues.Rd
man/trimWhitespace.Rd
man/ttest.Rd
man/uniqueBy.Rd
man/updateClinicalParams.Rd
man/updateProgress.Rd
man/vennEvents.Rd
man/wilcox.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/testDifferentialSplicing.R
tests/testthat/testFilterGroups.R
tests/testthat/testFirebrowse.R
tests/testthat/testGeneInfo.R
tests/testthat/testGroups.R
tests/testthat/testLeveneTest.R
tests/testthat/testLoadBy.R
tests/testthat/testMatsEvents.R
tests/testthat/testMisoEvents.R
tests/testthat/testPCA.R
tests/testthat/testPSIquantification.R
tests/testthat/testRenameDuplicated.R
tests/testthat/testRowVar.R
tests/testthat/testSuppaEvents.R
tests/testthat/testSurvival.R
tests/testthat/testUtils.R
tests/testthat/testVastToolsEvents.R
vignettes
vignettes/AS_events_preparation.Rmd
vignettes/BRCA_clinical.RDS
vignettes/BRCA_psi.RDS
vignettes/CLI_tutorial.Rmd
vignettes/GUI_tutorial.Rmd
vignettes/img
vignettes/img/1_load_data.png
vignettes/img/2_quantify_splicing.png
vignettes/img/3_survival.png
vignettes/img/4_pca.png
vignettes/img/5_psi_cutoff_2.png
vignettes/img/6_diff_splicing.png
vignettes/img/7_psi_cutoff.png
vignettes/refs.bib
psichomics documentation built on May 20, 2017, 10:55 p.m.