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

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.

AuthorNuno 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], Bernardo Almeida [ctb]
Date of publicationNone
MaintainerNuno Saraiva-Agostinho <nunodanielagostinho@gmail.com>
LicenseMIT + file LICENSE
Version1.0.8
https://github.com/nuno-agostinho/psichomics

View on Bioconductor

Man pages

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

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

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

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

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

getDifferentialAnalysesSurvival: Get the table of differential analyses' survival data 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...

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

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

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...

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

parseTcgaSampleInfo: Parse and prepare sample information from TCGA samples

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 another vector

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

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

setDifferentialAnalysesSurvival: Set the table of differential analyses' survival data 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

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

settingsServer: Server logic of the settings

settingsUI: User interface of the settings

setURLtoDownload: Set URL links to download

showAlert: Show 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...

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

Files

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_gtex.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_firehoseJunctionReads.R psichomics/R/formats_firehoseMergeClinical.R psichomics/R/formats_gtexClinical.R psichomics/R/formats_gtexJunctionReads.R psichomics/R/formats_gtexSampleInfo.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/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/browserHistory.Rd psichomics/man/bsModal2.Rd psichomics/man/calculateInclusionLevels.Rd psichomics/man/checkFileFormat.Rd psichomics/man/checkFirebrowse.Rd psichomics/man/checkIntegrity.Rd psichomics/man/checkSurvivalInput.Rd psichomics/man/closeProgress.Rd psichomics/man/createDataTab.Rd psichomics/man/createDensitySparklines.Rd psichomics/man/createGroup.Rd psichomics/man/createGroupByAttribute.Rd psichomics/man/createGroupByColumn.Rd psichomics/man/createGroupById.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/getAutoNavigation.Rd psichomics/man/getCategories.Rd psichomics/man/getCategory.Rd psichomics/man/getCategoryData.Rd psichomics/man/getClinicalData.Rd psichomics/man/getClinicalMatchFrom.Rd psichomics/man/getColumnsTime.Rd psichomics/man/getCores.Rd psichomics/man/getData.Rd psichomics/man/getDataRows.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/getPSIperPatient.Rd psichomics/man/getPatientFromSample.Rd psichomics/man/getPatientId.Rd psichomics/man/getPrecision.Rd psichomics/man/getSampleId.Rd psichomics/man/getSampleInfo.Rd psichomics/man/getSelectedGroups.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/groupByAttribute.Rd psichomics/man/groupByExpression.Rd psichomics/man/groupByGrep.Rd psichomics/man/groupById.Rd psichomics/man/groupPerPatient.Rd psichomics/man/groupPerSample.Rd psichomics/man/groupsServer.Rd psichomics/man/groupsServerOnce.Rd psichomics/man/groupsUI.Rd psichomics/man/gtexDataServer.Rd psichomics/man/gtexDataUI.Rd psichomics/man/hc_scatter.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/loadGtexData.Rd psichomics/man/loadLocalFiles.Rd psichomics/man/loadedDataModal.Rd psichomics/man/localDataServer.Rd psichomics/man/localDataUI.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/parseTcgaSampleInfo.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/setAutoNavigation.Rd psichomics/man/setCategory.Rd psichomics/man/setClinicalMatchFrom.Rd psichomics/man/setCores.Rd psichomics/man/setData.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/setPatientId.Rd psichomics/man/setPrecision.Rd psichomics/man/setSampleId.Rd psichomics/man/setSampleInfo.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/showGroupsTable.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/BRCA_clinical.RDS
psichomics/vignettes/BRCA_psi.RDS
psichomics/vignettes/CLI_tutorial.Rmd
psichomics/vignettes/GUI_tutorial.Rmd
psichomics/vignettes/diff_splicing.png
psichomics/vignettes/load_data.png
psichomics/vignettes/pca.png
psichomics/vignettes/psi_cutoff.png
psichomics/vignettes/psi_cutoff_2.png
psichomics/vignettes/quantify_splicing.png
psichomics/vignettes/refs.bib
psichomics/vignettes/survival.png

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