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A B C D E F G H I J K L M N O P Q R S T U V W
| 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 the app All the CSS modifications are in the file "shiny/www/styles.css" |
| 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 annotation and junction quantification for many samples |
| checkFileFormat | Checks the format of a file |
| checkFirebrowse | Return an user interface depending on the status of the Firebrowse API |
| checkIntegrity | Compute the 32-byte MD5 hashes of one or more files and check with given md5 file |
| 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 interface) |
| 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 given column from a dataset |
| createGroupByColumn | Create groups with the indexes from the unique values of a given column from a dataset |
| 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 events |
| diffSplicingEventServer | Server logic for the analyses of a single alternative splicing event |
| 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 |
| errorAlert | Show an alert |
| errorModal | Style and show a modal |
| 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 results |
| fligner | Perform Fligner-Killeen test and return interface to show the results |
| 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 data category |
| 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 available and parse the response |
| getGlobal | Get data from global data |
| getGroupsFrom | Get groups from a given data type |
| getInclusionLevels | Get alternative splicing quantification of the selected data category |
| 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 matching the given index |
| getNumerics | Convert a column to numeric if possible and ignore given columns composed of lists |
| getPatientFromSample | Match given sample identifiers and return the respective row in clinical data |
| getPatientId | Get the identifier of patients for a given category |
| getPrecision | Get number of decimal places |
| getPSIperPatient | Assign alternative splicing quantification to patients based on their samples |
| 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 validator |
| 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 module |
| inclusionLevelsUI | Interface of the alternative splicing event quantification module |
| infoModal | Style and show a modal |
| infoServer | Server logic |
| infoUI | Information's user interface |
| insideFile | Get psichomics file inside a given directory |
| is.whole | Check if a number is whole |
| isFirehoseUp | Check if the Firehose API is running |
| joinEventsPerType | Full outer join all given events based on select columns |
| junctionString | String used to search for matches in a junction quantification file |
| kruskal | Perform Kruskal's test and return interface to show the results |
| labelBasedOnCutoff | Label groups based on a given cut-off |
| levene | Perform Levene's test and return interface to show the results |
| leveneTest | Levene's test |
| listAllAnnotations | List alternative splicing annotation files available, as well as custom annotation |
| 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 module |
| 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 it into R |
| loadFirehoseFolders | Load Firehose folders |
| loadGtexData | Load GTEx data given input |
| loadLocalFiles | Load local files |
| loadRequiredData | Missing information modal template |
| localDataServer | Server logic to load local data |
| localDataUI | Interface to load local data |
| missingDataGuide | Missing information modal template |
| 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 to separate survival curves |
| optimSurvDiff | Optimal survival difference given an inclusion level cut-off for a specific alternative splicing event |
| optimSurvDiffOptions | Interface for calculating optimal cut-off and p-value for survival curves differences |
| parseDateResponse | Parse the date from a response |
| parseFirehoseMetadata | Query the Firehose API for metadata and parse the response |
| parseMatsA3SS | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsA5SS | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsAFE | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsALE | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsAnnotation | Get events from alternative splicing annotation |
| parseMatsEvent | Parse alternative splicing events from MATS |
| parseMatsGeneric | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsMXE | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsRI | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMatsSE | Parse junctions of an alternative splicing event from MATS according to event type |
| parseMisoA3SS | Parse junctions of an event from MISO according to event type |
| parseMisoA5SS | Parse junctions of an event from MISO according to event type |
| parseMisoAFE | Parse junctions of an event from MISO according to event type |
| parseMisoALE | Parse junctions of an event from MISO according to event type |
| 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 alternative splicing annotation file and get events in a data frame |
| parseMisoGeneric | Parse junctions of an event from MISO according to event type |
| parseMisoId | Parse MISO's alternative splicing event identifier |
| parseMisoMXE | Parse junctions of an event from MISO according to event type |
| parseMisoRI | Parse junctions of an event from MISO according to event type |
| parseMisoSE | Parse junctions of an event from MISO according to event type |
| parseMisoTandemUTR | Parse junctions of an event from MISO according to event type |
| parseSampleGroups | Return the type of a given sample |
| parseSplicingEvent | Parse an alternative splicing event based on a given identifier |
| parseSuppaA3SS | Parse junctions of an event from SUPPA |
| parseSuppaA5SS | Parse junctions of an event from SUPPA |
| parseSuppaAFE | Parse junctions of an event from SUPPA |
| parseSuppaALE | Parse junctions of an event from SUPPA |
| parseSuppaAnnotation | Get events from alternative splicing annotation |
| parseSuppaEvent | Parses splicing events of a specific event type from SUPPA |
| parseSuppaGeneric | Parse junctions of an event from SUPPA |
| parseSuppaMXE | Parse junctions of an event from SUPPA |
| parseSuppaRI | Parse junctions of an event from SUPPA |
| parseSuppaSE | 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 |
| parseVastToolsA3SS | Parse junctions of an event from VAST-TOOLS according to event type |
| parseVastToolsA5SS | Parse junctions of an event from VAST-TOOLS according to event type |
| parseVastToolsAnnotation | Get events from alternative splicing annotation |
| parseVastToolsEvent | Parses an alternative splicing event from VAST-TOOLS |
| parseVastToolsRI | Parse junctions of an event from VAST-TOOLS according to event type |
| parseVastToolsSE | Parse junctions of an event from VAST-TOOLS according to event type |
| pcaServer | Server logic for the principal component analysis |
| pcaUI | User interface of the principal component analysis |
| performPCA | Perform principal component analysis after processing missing values from data frame |
| 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 errors |
| 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 gene |
| quantifySplicing | Quantify alternative splicing events |
| queryEnsembl | Query the Ensembl REST API |
| queryEnsemblByEvent | Query information from Ensembl by a given alternative splicing event |
| 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 data category |
| 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 results |
| 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 processed survival terms |
| survfit.survTerms | Compute estime of a survival curve using processed survival terms |
| survivalServer | Server logic of survival analysis |
| survivalUI | User interface of survival analysis |
| tabDataset | Creates a tabPanel template for a datatable with a title and description |
| 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 given a cutoff |
| textSuggestions | Create script for autocompletion of text input |
| timePerPatient | Get all columns matching a given string and return a single vector with the max time for each patient if available |
| trimWhitespace | Trims whitespace from a word |
| ttest | Perform unpaired t-test analysis and return interface to show the results |
| uniqueBy | Check unique rows of a data frame based on a set of its columns |
| updateClinicalParams | Update available clinical attributes when the clinical data changes |
| updateProgress | Update a progress object |
| vennEvents | Compare the number of events from the different programs in a Venn diagram |
| warningAlert | Show an alert |
| warningModal | Style and show a modal |
| wilcox | Perform Wilcoxon analysis and return interface to show the results |