Package: psichomics 1.39.1

Nuno Saraiva-Agostinho

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

Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.

Authors:Nuno Saraiva-Agostinho [aut, cre], Nuno Luís 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 de Almeida [ctb]

psichomics_1.39.1.tar.gz
psichomics_1.39.1.zip(r-4.7)psichomics_1.39.1.zip(r-4.6)psichomics_1.39.1.zip(r-4.5)
psichomics_1.39.1.tgz(r-4.6-x86_64)psichomics_1.39.1.tgz(r-4.6-arm64)psichomics_1.39.1.tgz(r-4.5-x86_64)psichomics_1.39.1.tgz(r-4.5-arm64)
psichomics_1.39.1.tar.gz(r-4.7-arm64)psichomics_1.39.1.tar.gz(r-4.7-x86_64)psichomics_1.39.1.tar.gz(r-4.6-arm64)psichomics_1.39.1.tar.gz(r-4.6-x86_64)
psichomics_1.39.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
psichomics/json (API)

# Install 'psichomics' in R:
install.packages('psichomics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nuno-agostinho/psichomics/issues

Pkgdown/docs site:https://nuno-agostinho.github.io

Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:psichomics-1.39.1(bioc 3.24)psichomics-1.38.1(bioc 3.23)

sequencingrnaseqalternativesplicingdifferentialsplicingtranscriptionguiprincipalcomponentsurvivalbiomedicalinformaticstranscriptomicsimmunooncologyvisualizationmultiplecomparisongeneexpressiondifferentialexpressionalternative-splicingbioconductordata-analysesdifferential-gene-expressiondifferential-splicing-analysisgene-expressiongtexrecount2rna-seq-datasplicing-quantificationsratcgavast-toolscpp

7.30 score 37 stars 34 scripts 1 mentions 89 exports 195 dependencies

Last updated from:be77daf8cf. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING345
linux-devel-arm64NOTE906
linux-devel-x86_64NOTE649
source / vignettesOK441
linux-release-arm64NOTE684
linux-release-x86_64NOTE661
macos-release-arm64NOTE928
macos-release-x86_64NOTE805
macos-oldrel-arm64NOTE402
macos-oldrel-x86_64NOTE1297
windows-develNOTE1005
windows-releaseNOTE744
windows-oldrelNOTE527
wasm-releaseOK278

Exports:assignValuePerPatientassignValuePerSubjectcalculateLoadingsContributioncolSumsconvertGeneIdentifierscorrelateGEandAScreateGroupByAttributediffAnalysesdiscardLowCoveragePSIvaluesensemblToUniprotfilterGeneExprfilterGroupsfilterPSIgetAttributesTimegetDownloadsFoldergetFirebrowseCohortsgetFirebrowseDataTypesgetFirebrowseDatesgetGeneListgetGenesFromSplicingEventsgetGtexDataTypesgetGtexReleasesgetGtexTissuesgetMatchingSamplesgetPatientFromSamplegetSampleFromPatientgetSampleFromSubjectgetSplicingEventDatagetSplicingEventFromGenesgetSplicingEventTypesgetSubjectFromSamplegetTCGAcohortsgetTCGAdataTypesgetTCGAdatesgetValuePerPatientgetValuePerSubjectgroupPerElemisFirebrowseUplabelBasedOnCutofflistSplicingAnnotationsloadAnnotationloadFirebrowseDataloadGtexDataloadLocalFilesloadSRAprojectloadTCGAdatanormaliseGeneExpressionnormalizeGeneExpressionoptimalSurvivalCutoffparseCategoricalGroupsparseMatsAnnotationparseMisoAnnotationparseSampleGroupsparseSplicingEventparseSuppaAnnotationparseTcgaSampleInfoparseTCGAsampleInfoparseTCGAsampleTypesparseVastToolsAnnotationperformICAperformPCAplotCorrelationplotDistributionplotGeneExprPerSampleplotGroupIndependenceplotICAplotLibrarySizeplotPCAplotPCAvarianceplotProteinplotRowStatsplotSplicingEventplotSurvivalCurvesplotSurvivalPvaluesByCutoffplotTranscriptsplotVarianceprepareAnnotationFromEventsprepareGeneQuantprepareJunctionQuantprepareSRAmetadataprocessSurvTermspsichomicsquantifySplicingqueryEnsemblByEventqueryEnsemblByGenereadFilesurvdiffTermstestGroupIndependencetestSurvival

Dependencies:abindAnnotationDbiAnnotationHubaskpassassertthatbackportsbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionBiostringsbitbit64bitopsblobbroomBSgenomebslibbumphuntercachemcheckmatecigarilloclicliprclustercodetoolscolorspacecolourpickercommonmarkcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayderfinderderfinderHelperdigestdoRNGdownloaderdplyrDTedgeRevaluatefarverfastICAfastmapfastmatchfilelockfontawesomeforeachforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicFilesGenomicRangesGEOqueryggplot2ggrepelgluegridExtragtablehighcharterhighrHmischmshtmlTablehtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobanditeratorsjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalocfitlubridatemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeminiUInnetopensslotelpairsD3pillarpkgconfigplyrpngprettyunitsprogresspromisespurrrquantmodqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppParallelRCurlreadrrecountrentrezreshape2restfulrRfastRhtslibrjsonrlangrlistrmarkdownrngtoolsrpartRsamtoolsRSQLiterstudioapirtracklayerrvestS4ArraysS4VectorsS7sassscalesselectrSeqinfoshinyshinyBSshinyjssnowsourcetoolsSparseArraystatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetinytexTTRtzdbUCSC.utilsutf8VariantAnnotationvctrsviridisLitevroomwithrxfunXMLxml2xtablextsXVectoryamlziggzoo

Case study: command-line interface (CLI) tutorial
Installing and starting the program | Quick reference of psichomics functions | Exploration of clinically-relevant, differentially spliced events in breast cancer | Downloading and loading TCGA data | Filtering and normalising gene expression | Quantifying alternative splicing | Data grouping | Principal component analysis (PCA) | NUMB exon 12 inclusion and correlation with QKI gene expression | Differential inclusion of NUMB exon 12 | Correlation between NUMB exon 12 inclusion and QKI expression | Differential splicing analysis | Performing multiple survival analysis | Differential gene expression | UHRF2 exon 10 inclusion | Survival analysis | Differential expression | Literature support and external database information | Interpretation | Loading data from other sources | Load GTEx data | Load SRA project data using recount | Load user-provided data | Feedback | References
Rendered fromCLI_tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-01-07
Started: 2016-09-07

Case study: visual interface tutorial
Installing and starting the program | Exploration of clinically-relevant, differentially spliced events in breast cancer | Downloading and loading TCGA data | Filtering and normalising gene expression | Quantifying alternative splicing | Data grouping | Principal component analysis (PCA) | PCA performance | PCA plotting | NUMB exon 12 inclusion and correlation with QKI gene expression | Differential inclusion of NUMB exon 12 | Correlation between NUMB exon 12 inclusion and QKI expression | Differential splicing analysis | Filtering alternative splicing events | Performing multiple survival analysis | Differential gene expression | UHRF2 exon 10 inclusion | Survival analysis | Differential expression | Literature support and external database information | Interpretation | Exploring alternative splicing changes between human isogenic stem cells and fibroblasts | Load SRA and user-provided local files | Feedback | References
Rendered fromGUI_tutorial.Rmdusingknitr::rmarkdown

Last update: 2026-01-07
Started: 2016-09-07

Loading user-provided data
Supported file formats | Prepare SRA Run Selector data | Prepare tables based on RNA-seq data using STAR | Download FASTQ files (optional) | Align RNA-seq data to quantify splice junctions | Index the genome using STAR | Align against genome index using STAR | Prepare output for psichomics | Prepare VAST-TOOLS data | Prepare FireBrowse data | Prepare GTEx data | Prepare data from any source | Sample information | Subject information | Gene expression | Exon-exon junction quantification | Alternative splicing quantification (also known as inclusion levels) | Load user-provided data into psichomics | Load using the visual interface | Load using the command-line interface (CLI) | Feedback | References
Rendered fromcustom_data.Rmdusingknitr::rmarkdown

Last update: 2026-01-07
Started: 2019-03-27

Preparing an Alternative Splicing Annotation for psichomics
Creating custom alternative splicing annotation | SUPPA annotation | rMATS annotation | MISO annotation | VAST-TOOLS annotation | Combining annotation from different sources | Quantifying alternative splicing using the custom annotation | Feedback
Rendered fromAS_events_preparation.Rmdusingknitr::rmarkdown

Last update: 2026-01-07
Started: 2016-10-08

Readme and manuals

Help Manual

Help pageTopics
Print startup message.onAttach
Display results of correlation analysesas.table.GEandAScorrelation plot.GEandAScorrelation plotCorrelation print.GEandAScorrelation [.GEandAScorrelation
Assign average sample values to their corresponding subjectsassignValuePerPatient assignValuePerSubject getValuePerPatient getValuePerSubject
Calculate the contribution of PCA loadings to the selected principal componentscalculateLoadingsContribution
Sum columns using an 'EList-class' objectcolSums,EList-method
Convert gene identifiersconvertGeneIdentifiers
Correlate gene expression data against alternative splicing quantificationcorrelateGEandAS
Split elements into groups based on a given column of a datasetcreateGroupByAttribute
Perform statistical analysesdiffAnalyses
Remove alternative splicing quantification values based on coveragediscardLowCoveragePSIvalues
Convert from Ensembl to UniProt identifierensemblToUniprot
Filter genes based on their expressionfilterGeneExpr
Filter groups with less data points than the thresholdfilterGroups
Filter alternative splicing quantificationfilterPSI
Get time values for given columns in a clinical datasetgetAttributesTime
Get the path to the Downloads foldergetDownloadsFolder
Get curated, literature-based gene listsgetGeneList
Get GTEx data informationgetGtexDataTypes getGtexReleases
Get GTEx tissues from given GTEx sample attributesgetGtexTissues
Get samples matching the given subjectsgetMatchingSamples getSampleFromPatient getSampleFromSubject
Get splicing event information for given alternative splicing quantification datagetSplicingEventData
Get alternative splicing events from genes or vice-versagetGenesFromSplicingEvents getSplicingEventFromGenes
Get supported splicing event typesgetSplicingEventTypes
Get subjects from given samplesgetPatientFromSample getSubjectFromSample
Get available parameters for TCGA datagetFirebrowseCohorts getFirebrowseDataTypes getFirebrowseDates getTCGAcohorts getTCGAdataTypes getTCGAdates
Assign one group to each elementgroupPerElem
Check if FireBrowse API is runningisFirebrowseUp
Label groups based on a given cutofflabelBasedOnCutoff
List alternative splicing annotationslistSplicingAnnotations
Load alternative splicing annotation from 'AnnotationHub'loadAnnotation
Download and load GTEx dataloadGtexData
Load local filesloadLocalFiles
Download and load SRA projects via recount2loadSRAproject
Download and process TCGA dataloadFirebrowseData loadTCGAdata
Filter and normalise gene expressionnormaliseGeneExpression normalizeGeneExpression
Calculate optimal data cutoff that best separates survival curvesoptimalSurvivalCutoff
Parse categorical columns in a data frameparseCategoricalGroups
Parse alternative splicing event identifierparseSplicingEvent
Parse events from alternative splicing annotationparseMatsAnnotation parseMisoAnnotation parseSuppaAnnotation parseVastToolsAnnotation
Parse sample information from TCGA sample identifiersparseSampleGroups parseTCGAsampleInfo parseTcgaSampleInfo parseTCGAsampleTypes
Perform independent component analysis after processing missing valuesperformICA
Perform principal component analysis after processing missing valuesperformPCA
Plot sample distributionplotDistribution
Plot distribution of gene expression per sampleplotGeneExprPerSample
Plot '-log10(p-values)' of the results obtained after multiple group independence testingplotGroupIndependence
Create multiple scatterplots from ICAplotICA
Plot library sizeplotLibrarySize
Create a scatterplot from a PCA objectplotPCA
Create the explained variance plot from a PCAplotPCAvariance plotVariance
Plot protein featuresplotProtein
Plot row-wise statisticsplotRowStats
Plot diagram of alternative splicing eventsplotSplicingEvent
Plot survival curvesplotSurvivalCurves
Plot p-values of survival difference between groups based on multiple cutoffsplotSurvivalPvaluesByCutoff
Plot transcriptsplotTranscripts
Prepare annotation from alternative splicing eventsprepareAnnotationFromEvents
Prepare user-provided files to be loaded into psichomicsprepareGeneQuant prepareJunctionQuant prepareSRAmetadata
Process survival curves terms to calculate survival curvesprocessSurvTerms
Start graphical interface of psichomicspsichomics
Quantify alternative splicing eventsquantifySplicing
Query information from EnsemblqueryEnsemblByEvent queryEnsemblByGene
Load psichomics-specific filereadFile
Test Survival Curve DifferencessurvdiffTerms
Create survival curvessurvfit.survTerms
Preserve attributes of 'sticky' objects when extracting or transposing objectt.sticky [.sticky
Multiple independence tests between reference groups and list of groupstestGroupIndependence
Test the survival difference between groups of subjectstestSurvival