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

Share:

Package with a Shiny-based graphical interface for the integrated analysis of alternative splicing data from The Cancer Genome Atlas (TCGA). 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 samples.

Author
Nuno Saraiva Agostinho [aut, cre], Nuno Barbosa Morais [aut, ths], André Falcão [ths], Lina Gallego Paez [ctb], Marie Bordone [ctb], Teresa Maia [ctb], Mariana Ferreira [ctb], Ana Carolina Leote [ctb]
Date of publication
None
Maintainer
Nuno Saraiva Agostinho <nunodanielagostinho@gmail.com>
License
MIT + file LICENSE
Version
1.0.2
URLs

View on Bioconductor

Man pages

addLocalFile
Creates a UI set with options to add a file from the local...
addTCGAdata
Creates a UI set with options to add data from TCGA/Firehose
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
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...
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
createGroupByColumn
Create groups with the indexes from the unique values of a...
createGroupByRows
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
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
escape
Escape symbols for use in regular expressions
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
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
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
getDifferentialAnalysesSurvival
Get the table of differential analyses' survival data of a...
getDiffSplicingGroups
Get the groups column for differential splicing analysis of a...
getDownloadsFolder
Get the Downloads folder of the user
getEvent
Get selected alternative splicing event's identifer
getFirehoseCohorts
Query the Firehose API for the cohorts available
getFirehoseDataTypes
Get data types available from Firehose
getFirehoseDateFormat
Returns the date format used by the Firehose API
getFirehoseDates
Query the Firehose 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...
getPrecision
Get number of decimal places
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
groupByColumn
User interface to group by column
groupByExpression
User interface to group by subset expression
groupByGrep
User interface to group by grep expression
groupByRow
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
groupsUI
Creates UI elements for the grouping feature
hchart.survfit
Plot survival curves using Highcharts
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
isFirehoseUp
Check if the Firehose 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
loadFirehoseData
Downloads and processes data from the Firehose API and loads...
loadFirehoseFolders
Load Firehose folders
loadLocalFiles
Load local files
localDataServer
Server logic 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...
optimSurvDiffOptions
Interface for calculating optimal cut-off and p-value for...
parseDateResponse
Parse the date from a response
parseFirehoseMetadata
Query the Firehose API for metadata and parse the response
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
parseUniprotXML
Parse XML from Uniprot's RESTful service
parseUrlsFromFirehoseResponse
Retrieve URLs from a response to a Firehose 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
plotProtein
Plot protein features
plotSurvivalCurves
Plot survival curves
plotTranscripts
Plot transcripts
plotVariance
Create the explained variance plot
prepareAnnotationFromEvents
Prepare annotation from alternative splicing events
prepareFirehoseArchives
Prepares Firehose 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
queryFirehoseData
Query the Firehose 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 comparison
renameGroups
Rename duplicated names from a new group
renderDataTableSparklines
Render a data table with Sparkline HTML elements
renderGeneticInfo
Render genetic 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
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
setDifferentialAnalysesSurvival
Set the table of differential analyses' survival data of a...
setDiffSplicingGroups
Set the groups column for differential splicing analysis of a...
setEvent
Set event
setFirehoseData
Set data from Firehose
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
setPrecision
Set number of decimal places
setSignificant
Set number of significant digits
setSpecies
Set the species of a data category
settingsServer
Server logic of the settings
settingsUI
User interface of the settings
setURLtoDownload
Set URL links to download
showAlert
Show an alert
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...
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...

Files in this package

psichomics/DESCRIPTION
psichomics/LICENSE
psichomics/NAMESPACE
psichomics/NEWS
psichomics/R
psichomics/R/analysis.R
psichomics/R/analysis_diffSplicing.R
psichomics/R/analysis_diffSplicing_event.R
psichomics/R/analysis_diffSplicing_table.R
psichomics/R/analysis_information.R
psichomics/R/analysis_pca.R
psichomics/R/analysis_survival.R
psichomics/R/analysis_template.R
psichomics/R/app.R
psichomics/R/data.R
psichomics/R/data_firebrowse.R
psichomics/R/data_inclusionLevels.R
psichomics/R/data_local.R
psichomics/R/events.R
psichomics/R/events_mats.R
psichomics/R/events_miso.R
psichomics/R/events_suppa.R
psichomics/R/events_vastTools.R
psichomics/R/formats.R
psichomics/R/formats_firehoseGeneExpression.R
psichomics/R/formats_firehoseJunctionQuantification.R
psichomics/R/formats_firehoseMergeClinical.R
psichomics/R/globalAccess.R
psichomics/R/groups.R
psichomics/R/settings.R
psichomics/R/utils.R
psichomics/README.md
psichomics/build
psichomics/build/vignette.rds
psichomics/inst
psichomics/inst/doc
psichomics/inst/doc/AS_events_preparation.R
psichomics/inst/doc/AS_events_preparation.Rmd
psichomics/inst/doc/AS_events_preparation.html
psichomics/inst/doc/CLI_tutorial.R
psichomics/inst/doc/CLI_tutorial.Rmd
psichomics/inst/doc/CLI_tutorial.html
psichomics/inst/doc/GUI_tutorial.R
psichomics/inst/doc/GUI_tutorial.Rmd
psichomics/inst/doc/GUI_tutorial.html
psichomics/inst/extdata
psichomics/inst/extdata/TCGAsampleType.RDS
psichomics/inst/extdata/eventsAnnotSample
psichomics/inst/extdata/eventsAnnotSample/VASTDB
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.ALT3.Template.txt
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.ALT5.Template.txt
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.COMBI.Template.txt
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.EXSK.Template.2.txt
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.IR.Template.txt
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MERGE3m.Template.txt
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MIC.Template.txt
psichomics/inst/extdata/eventsAnnotSample/VASTDB/Hsa/TEMPLATES/Hsa.MULTI.Template.2.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.A3SS.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.A5SS.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.AFE.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.ALE.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.MXE.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.RI.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.SE.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.A3SS.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.A5SS.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.AFE.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.ALE.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.MXE.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.RI.txt
psichomics/inst/extdata/eventsAnnotSample/mats_output/ASEvents/fromGTF.novelEvents.SE.txt
psichomics/inst/extdata/eventsAnnotSample/miso_annotation
psichomics/inst/extdata/eventsAnnotSample/miso_annotation/A3SS.hg19.gff3
psichomics/inst/extdata/eventsAnnotSample/miso_annotation/A5SS.hg19.gff3
psichomics/inst/extdata/eventsAnnotSample/miso_annotation/AFE.hg19.gff3
psichomics/inst/extdata/eventsAnnotSample/miso_annotation/ALE.hg19.gff3
psichomics/inst/extdata/eventsAnnotSample/miso_annotation/MXE.hg19.gff3
psichomics/inst/extdata/eventsAnnotSample/miso_annotation/RI.hg19.gff3
psichomics/inst/extdata/eventsAnnotSample/miso_annotation/SE.hg19.gff3
psichomics/inst/extdata/eventsAnnotSample/miso_annotation/TandemUTR.hg19.gff3
psichomics/inst/extdata/eventsAnnotSample/suppa_output
psichomics/inst/extdata/eventsAnnotSample/suppa_output/suppaEvents
psichomics/inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_A3.ioe
psichomics/inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_A5.ioe
psichomics/inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_AF.ioe
psichomics/inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_AL.ioe
psichomics/inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_MX.ioe
psichomics/inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_RI.ioe
psichomics/inst/extdata/eventsAnnotSample/suppa_output/suppaEvents/hg19_SE.ioe
psichomics/inst/extdata/ex_junctionQuant.RDS
psichomics/inst/extdata/ex_splicing_annotation.RDS
psichomics/inst/extdata/miso_AS_annot_example.gff3
psichomics/inst/shiny
psichomics/inst/shiny/www
psichomics/inst/shiny/www/animate.min.css
psichomics/inst/shiny/www/functions.js
psichomics/inst/shiny/www/fuzzy.min.js
psichomics/inst/shiny/www/jquery.textcomplete.min.js
psichomics/inst/shiny/www/styles.css
psichomics/inst/shiny/www/validator.min.js
psichomics/man
psichomics/man/addLocalFile.Rd
psichomics/man/addTCGAdata.Rd
psichomics/man/analysesServer.Rd
psichomics/man/analysesUI.Rd
psichomics/man/appServer.Rd
psichomics/man/appUI.Rd
psichomics/man/articleUI.Rd
psichomics/man/basicStats.Rd
psichomics/man/bsModal2.Rd
psichomics/man/calculateInclusionLevels.Rd
psichomics/man/checkFileFormat.Rd
psichomics/man/checkFirebrowse.Rd
psichomics/man/checkIntegrity.Rd
psichomics/man/closeProgress.Rd
psichomics/man/createDataTab.Rd
psichomics/man/createDensitySparklines.Rd
psichomics/man/createGroupByColumn.Rd
psichomics/man/createGroupByRows.Rd
psichomics/man/createGroupFromInput.Rd
psichomics/man/createJunctionsTemplate.Rd
psichomics/man/dataServer.Rd
psichomics/man/dataUI.Rd
psichomics/man/diffAnalyses.Rd
psichomics/man/diffSplicingEventServer.Rd
psichomics/man/diffSplicingEventUI.Rd
psichomics/man/diffSplicingServer.Rd
psichomics/man/diffSplicingTableServer.Rd
psichomics/man/diffSplicingTableUI.Rd
psichomics/man/diffSplicingUI.Rd
psichomics/man/disableTab.Rd
psichomics/man/downloadFiles.Rd
psichomics/man/echoProgress.Rd
psichomics/man/enableTab.Rd
psichomics/man/endProcess.Rd
psichomics/man/ensemblToUniprot.Rd
psichomics/man/escape.Rd
psichomics/man/export_highcharts.Rd
psichomics/man/filterGroups.Rd
psichomics/man/firebrowseUI.Rd
psichomics/man/fisher.Rd
psichomics/man/fligner.Rd
psichomics/man/getActiveDataset.Rd
psichomics/man/getAssemblyVersion.Rd
psichomics/man/getCategories.Rd
psichomics/man/getCategory.Rd
psichomics/man/getCategoryData.Rd
psichomics/man/getClinicalData.Rd
psichomics/man/getClinicalMatchFrom.Rd
psichomics/man/getCores.Rd
psichomics/man/getData.Rd
psichomics/man/getDataRows.Rd
psichomics/man/getDiffSplicingGroups.Rd
psichomics/man/getDifferentialAnalyses.Rd
psichomics/man/getDifferentialAnalysesSurvival.Rd
psichomics/man/getDownloadsFolder.Rd
psichomics/man/getEvent.Rd
psichomics/man/getFirehoseCohorts.Rd
psichomics/man/getFirehoseDataTypes.Rd
psichomics/man/getFirehoseDateFormat.Rd
psichomics/man/getFirehoseDates.Rd
psichomics/man/getGlobal.Rd
psichomics/man/getGroupsFrom.Rd
psichomics/man/getInclusionLevels.Rd
psichomics/man/getInclusionLevelsPCA.Rd
psichomics/man/getJunctionQuantification.Rd
psichomics/man/getMatchingSamples.Rd
psichomics/man/getNumerics.Rd
psichomics/man/getPatientFromSample.Rd
psichomics/man/getPrecision.Rd
psichomics/man/getServerFunctions.Rd
psichomics/man/getSignificant.Rd
psichomics/man/getSpecies.Rd
psichomics/man/getSplicingEventCoordinates.Rd
psichomics/man/getSplicingEventTypes.Rd
psichomics/man/getURLtoDownload.Rd
psichomics/man/getUiFunctions.Rd
psichomics/man/getValidEvents.Rd
psichomics/man/globalSelectize.Rd
psichomics/man/groupByColumn.Rd
psichomics/man/groupByExpression.Rd
psichomics/man/groupByGrep.Rd
psichomics/man/groupByRow.Rd
psichomics/man/groupPerPatient.Rd
psichomics/man/groupPerSample.Rd
psichomics/man/groupsServer.Rd
psichomics/man/groupsUI.Rd
psichomics/man/hchart.survfit.Rd
psichomics/man/inclusionLevelsInterface.Rd
psichomics/man/inclusionLevelsServer.Rd
psichomics/man/inclusionLevelsUI.Rd
psichomics/man/infoServer.Rd
psichomics/man/infoUI.Rd
psichomics/man/insideFile.Rd
psichomics/man/is.whole.Rd
psichomics/man/isFirehoseUp.Rd
psichomics/man/joinEventsPerType.Rd
psichomics/man/junctionString.Rd
psichomics/man/kruskal.Rd
psichomics/man/labelBasedOnCutoff.Rd
psichomics/man/levene.Rd
psichomics/man/leveneTest.Rd
psichomics/man/listAllAnnotations.Rd
psichomics/man/listSplicingAnnotations.Rd
psichomics/man/loadAnnotation.Rd
psichomics/man/loadBy.Rd
psichomics/man/loadFile.Rd
psichomics/man/loadFileFormats.Rd
psichomics/man/loadFirehoseData.Rd
psichomics/man/loadFirehoseFolders.Rd
psichomics/man/loadLocalFiles.Rd
psichomics/man/loadedDataModal.Rd
psichomics/man/localDataServer.Rd
psichomics/man/missingDataModal.Rd
psichomics/man/modTabPanel.Rd
psichomics/man/navSelectize.Rd
psichomics/man/noinfo.Rd
psichomics/man/operateOnGroups.Rd
psichomics/man/optimSurvDiff.Rd
psichomics/man/optimSurvDiffOptions.Rd
psichomics/man/optimalPSIcutoff.Rd
psichomics/man/parseDateResponse.Rd
psichomics/man/parseFirehoseMetadata.Rd
psichomics/man/parseMatsEvent.Rd
psichomics/man/parseMatsGeneric.Rd
psichomics/man/parseMisoAnnotation.Rd
psichomics/man/parseMisoEvent.Rd
psichomics/man/parseMisoEventID.Rd
psichomics/man/parseMisoGeneric.Rd
psichomics/man/parseMisoId.Rd
psichomics/man/parseSampleGroups.Rd
psichomics/man/parseSplicingEvent.Rd
psichomics/man/parseSuppaEvent.Rd
psichomics/man/parseSuppaGeneric.Rd
psichomics/man/parseUniprotXML.Rd
psichomics/man/parseUrlsFromFirehoseResponse.Rd
psichomics/man/parseValidFile.Rd
psichomics/man/parseVastToolsEvent.Rd
psichomics/man/parseVastToolsSE.Rd
psichomics/man/pcaServer.Rd
psichomics/man/pcaUI.Rd
psichomics/man/performPCA.Rd
psichomics/man/plotDistribution.Rd
psichomics/man/plotMiniSurvivalCurves.Rd
psichomics/man/plotPCA.Rd
psichomics/man/plotProtein.Rd
psichomics/man/plotSurvivalCurves.Rd
psichomics/man/plotTranscripts.Rd
psichomics/man/plotVariance.Rd
psichomics/man/prepareAnnotationFromEvents.Rd
psichomics/man/prepareFirehoseArchives.Rd
psichomics/man/processButton.Rd
psichomics/man/processDatasetNames.Rd
psichomics/man/processSurvData.Rd
psichomics/man/processSurvTerms.Rd
psichomics/man/processSurvival.Rd
psichomics/man/psichomics.Rd
psichomics/man/pubmedUI.Rd
psichomics/man/quantifySplicing.Rd
psichomics/man/queryEnsembl.Rd
psichomics/man/queryEnsemblByEvent.Rd
psichomics/man/queryEnsemblByGene.Rd
psichomics/man/queryFirehoseData.Rd
psichomics/man/queryPubMed.Rd
psichomics/man/queryUniprot.Rd
psichomics/man/readFile.Rd
psichomics/man/renameDuplicated.Rd
psichomics/man/renameGroups.Rd
psichomics/man/renderDataTableSparklines.Rd
psichomics/man/renderGeneticInfo.Rd
psichomics/man/rm.null.Rd
psichomics/man/roundDigits.Rd
psichomics/man/rowVar.Rd
psichomics/man/selectGroupsServer.Rd
psichomics/man/selectGroupsUI.Rd
psichomics/man/setActiveDataset.Rd
psichomics/man/setAssemblyVersion.Rd
psichomics/man/setCategory.Rd
psichomics/man/setClinicalMatchFrom.Rd
psichomics/man/setCores.Rd
psichomics/man/setData.Rd
psichomics/man/setDiffSplicingGroups.Rd
psichomics/man/setDifferentialAnalyses.Rd
psichomics/man/setDifferentialAnalysesSurvival.Rd
psichomics/man/setEvent.Rd
psichomics/man/setFirehoseData.Rd
psichomics/man/setGlobal.Rd
psichomics/man/setGroupsFrom.Rd
psichomics/man/setInclusionLevels.Rd
psichomics/man/setInclusionLevelsPCA.Rd
psichomics/man/setLocalData.Rd
psichomics/man/setPrecision.Rd
psichomics/man/setSignificant.Rd
psichomics/man/setSpecies.Rd
psichomics/man/setURLtoDownload.Rd
psichomics/man/settingsServer.Rd
psichomics/man/settingsUI.Rd
psichomics/man/showAlert.Rd
psichomics/man/signifDigits.Rd
psichomics/man/singleDiffAnalyses.Rd
psichomics/man/sortCoordinates.Rd
psichomics/man/spearman.Rd
psichomics/man/startProcess.Rd
psichomics/man/startProgress.Rd
psichomics/man/styleModal.Rd
psichomics/man/survdiff.survTerms.Rd
psichomics/man/survfit.survTerms.Rd
psichomics/man/survivalServer.Rd
psichomics/man/survivalUI.Rd
psichomics/man/tabDataset.Rd
psichomics/man/templateServer.Rd
psichomics/man/templateUI.Rd
psichomics/man/testSurvival.Rd
psichomics/man/testSurvivalCutoff.Rd
psichomics/man/textSuggestions.Rd
psichomics/man/timePerPatient.Rd
psichomics/man/trimWhitespace.Rd
psichomics/man/ttest.Rd
psichomics/man/uniqueBy.Rd
psichomics/man/updateClinicalParams.Rd
psichomics/man/updateProgress.Rd
psichomics/man/vennEvents.Rd
psichomics/man/wilcox.Rd
psichomics/tests
psichomics/tests/testthat
psichomics/tests/testthat.R
psichomics/tests/testthat/testDifferentialSplicing.R
psichomics/tests/testthat/testFilterGroups.R
psichomics/tests/testthat/testFirehose.R
psichomics/tests/testthat/testGeneInfo.R
psichomics/tests/testthat/testGroups.R
psichomics/tests/testthat/testLeveneTest.R
psichomics/tests/testthat/testLoadBy.R
psichomics/tests/testthat/testMatsEvents.R
psichomics/tests/testthat/testMisoEvents.R
psichomics/tests/testthat/testPCA.R
psichomics/tests/testthat/testPSIquantification.R
psichomics/tests/testthat/testRenameDuplicated.R
psichomics/tests/testthat/testRowVar.R
psichomics/tests/testthat/testSuppaEvents.R
psichomics/tests/testthat/testSurvival.R
psichomics/tests/testthat/testUtils.R
psichomics/tests/testthat/testVastToolsEvents.R
psichomics/vignettes
psichomics/vignettes/AS_events_preparation.Rmd
psichomics/vignettes/CLI_tutorial.Rmd
psichomics/vignettes/GUI_tutorial.Rmd
psichomics/vignettes/diff_splicing.png
psichomics/vignettes/ex_TCGA_clinical.RDS
psichomics/vignettes/ex_TCGA_junction_quant_chr22.RDS
psichomics/vignettes/load_data.png
psichomics/vignettes/pca.png
psichomics/vignettes/psi_cutoff.png
psichomics/vignettes/quantify_splicing.png
psichomics/vignettes/refs.bib
psichomics/vignettes/survival.png