{ "_id": "6a1befea1d7bb097a0a223ae", "Package": "psichomics", "Title": "Graphical Interface for Alternative Splicing Quantification,\nAnalysis and Visualisation", "Version": "1.39.1", "Encoding": "UTF-8", "Authors@R": "c(\nperson(\"Nuno\", \"Saraiva-Agostinho\",\nemail=\"nunodanielagostinho@gmail.com\", role=c(\"aut\", \"cre\"),\ncomment=c(ORCID=\"0000-0002-5549-105X\")),\nperson(c(\"Nuno\", \"Luís\"), \"Barbosa-Morais\", role=c(\"aut\", \"led\", \"ths\"),\ncomment=c(ORCID=\"0000-0002-1215-0538\")),\nperson(\"André\", \"Falcão\", role=\"ths\"),\nperson(\"Lina\", \"Gallego Paez\", role=\"ctb\"),\nperson(\"Marie\", \"Bordone\", role=\"ctb\"),\nperson(\"Teresa\", \"Maia\", role=\"ctb\"),\nperson(\"Mariana\", \"Ferreira\", role=\"ctb\"),\nperson(\"Ana Carolina\", \"Leote\", role=\"ctb\"),\nperson(\"Bernardo\", \"de Almeida\", role=\"ctb\"))", "Description": "Interactive R package with an intuitive Shiny-based\ngraphical interface for alternative splicing quantification and\nintegrative analyses of alternative splicing and gene\nexpression based on The Cancer Genome Atlas (TCGA), the\nGenotype-Tissue Expression project (GTEx), Sequence Read\nArchive (SRA) and user-provided data. The tool interactively\nperforms survival, dimensionality reduction and median- and\nvariance-based differential splicing and gene expression\nanalyses that benefit from the incorporation of clinical and\nmolecular sample-associated features (such as tumour stage or\nsurvival). Interactive visual access to genomic mapping and\nfunctional annotation of selected alternative splicing events\nis also included.", "License": "MIT + file LICENSE", "RoxygenNote": "7.3.3", "VignetteBuilder": "knitr", "Collate": "'RcppExports.R' 'utils.R' 'globalAccess.R' 'app.R'\n'analysis.R' 'analysis_correlation.R'\n'analysis_diffExpression.R' 'analysis_diffExpression_event.R'\n'analysis_diffExpression_table.R' 'analysis_diffSplicing.R'\n'analysis_diffSplicing_event.R' 'analysis_diffSplicing_table.R'\n'analysis_dimReduction.R' 'analysis_dimReduction_ica.R'\n'analysis_dimReduction_pca.R' 'analysis_information.R'\n'analysis_survival.R' 'analysis_template.R' 'data.R'\n'formats.R' 'data_firebrowse.R'\n'data_geNormalisationFiltering.R' 'data_gtex.R'\n'data_inclusionLevels.R' 'data_inclusionLevelsFilter.R'\n'data_local.R' 'data_recount.R' 'events_suppa.R'\n'events_vastTools.R' 'events_miso.R' 'events_mats.R' 'events.R'\n'formats_SraRunTableSampleInfo.R'\n'formats_firebrowseGeneExpression.R'\n'formats_firebrowseJunctionReads.R'\n'formats_firebrowseMergeClinical.R'\n'formats_firebrowseNormalizedGeneExpression.R'\n'formats_genericClinical.R' 'formats_genericGeneExpression.R'\n'formats_genericInclusionLevels.R'\n'formats_genericJunctionReads.R' 'formats_genericSampleInfo.R'\n'formats_gtexClinical.R' 'formats_gtexGeneReadsFormat.R'\n'formats_gtexJunctionReads.R' 'formats_gtexSampleInfo.R'\n'formats_gtexV7Clinical.R' 'formats_gtexV7JunctionReads.R'\n'formats_gtexV8JunctionReads.R'\n'formats_psichomicsGeneExpression.R'\n'formats_psichomicsInclusionLevels.R'\n'formats_recountSampleInfo.R'\n'formats_vasttoolsGeneExpression.R'\n'formats_vasttoolsInclusionLevels.R'\n'formats_vasttoolsInclusionLevelsTidy.R' 'groups.R' 'help.R'\n'utils_drawSplicingEvent.R' 'utils_eventParsing.R'\n'utils_fileBrowserDialog.R' 'utils_interactiveGgplot.R'\n'utils_interface.R'", "biocViews": "Sequencing, RNASeq, AlternativeSplicing,\nDifferentialSplicing, Transcription, GUI, PrincipalComponent,\nSurvival, BiomedicalInformatics, Transcriptomics,\nImmunoOncology, Visualization, MultipleComparison,\nGeneExpression, DifferentialExpression", "URL": "https://nuno-agostinho.github.io/psichomics/,\nhttps://github.com/nuno-agostinho/psichomics/", "BugReports": "https://github.com/nuno-agostinho/psichomics/issues", "Language": "en-GB", "Config/pak/sysreqs": "cmake libglpk-dev make libbz2-dev libicu-dev\nliblzma-dev libpng-dev libuv1-dev libxml2-dev libssl-dev\nlibx11-dev xz-utils zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-30 22:22:08 UTC", "RemoteUrl": "https://github.com/bioc/psichomics", "RemoteRef": "HEAD", "RemoteSha": "be77daf8cf983b7d0f0763aebdd70fc2f42d9c13", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-05-31 07:02:37 UTC", "User": "root" }, "Author": "Nuno Saraiva-Agostinho [aut, cre] (ORCID:\n),\nNuno Luís Barbosa-Morais [aut, led, ths] (ORCID:\n),\nAndré Falcão [ths],\nLina Gallego Paez [ctb],\nMarie Bordone [ctb],\nTeresa Maia [ctb],\nMariana Ferreira [ctb],\nAna Carolina Leote [ctb],\nBernardo de Almeida [ctb]", "Maintainer": "Nuno Saraiva-Agostinho ", "MD5sum": "4700801c54d7a28facda24978777c9eb", "_user": "bioc", "_type": "src", "_file": "psichomics_1.39.1.tar.gz", "_fileid": "ed8173f1f2662d939daa6d71775327e7c4483322b9ab79cf0bebbd098f6cd156", "_filesize": 6712079, "_sha256": "ed8173f1f2662d939daa6d71775327e7c4483322b9ab79cf0bebbd098f6cd156", "_created": "2026-05-31T07:02:37.000Z", "_published": "2026-05-31T08:23:06.395Z", "_jobs": [ { "job": 78707401169, "time": 300, "config": "bioc-checks", "r": "4.6.0", "check": "WARNING", "artifact": "7314676839" }, { "job": 78707401221, "time": 546, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7314702580" }, { "job": 78707401206, "time": 667, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7314716209" }, { "job": 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Author: Nuno Agostinho \n Date: Sun May 31 00:08:18 2026 +0200\n\n Merge pull request #489 from nuno-agostinho/performPCA-empty-input\n\n Handle empty inputs in `performPCA()` to prevent crashes\n\n commit dc206d7d9a50a8988b331e025a954612329c4fb5\n Author: Nuno Agostinho \n Date: Sat May 30 23:22:06 2026 +0200\n\n Handle empty inputs in `performPCA()` to prevent crashes\n\n commit f15b1eeeebcd2a1afda91efa9bf4944fc0c78d3e\n Merge: f2a3003c f9c2aac2\n Author: Nuno Agostinho \n Date: Mon May 11 09:26:45 2026 +0200\n\n Merge pull request #488 from nuno-agostinho/dependabot/docker/bioconductor/bioconductor_docker-3.23\n\n Bump bioconductor/bioconductor_docker from 3.22 to 3.23\n\n commit f9c2aac24d43b2041b0cbf38064258fe1b790c54\n Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>\n Date: Mon May 11 00:44:53 2026 +0000\n\n Bump bioconductor/bioconductor_docker from 3.22 to 3.23\n\n Bumps bioconductor/bioconductor_docker from 3.22 to 3.23.\n\n ---\n updated-dependencies:\n - dependency-name: bioconductor/bioconductor_docker\n dependency-version: '3.23'\n dependency-type: direct:production\n update-type: version-update:semver-minor\n ...\n\n Signed-off-by: dependabot[bot] \n\n commit f2a3003c3a46847a779952854df9218abfd14e95\n Merge: b12065f5 aeddd7d1\n Author: Nuno Agostinho \n Date: Wed Jan 7 11:15:53 2026 +0100\n\n Merge pull request #486 from nuno-agostinho/bump-1.36.1\n\n Bump version to 1.36.", "time": 1780179728 }, "_maintainer": { "name": "Nuno Saraiva-Agostinho", "email": "nunodanielagostinho@gmail.com", "login": "nuno-agostinho", "orcid": "0000-0002-5549-105X", "description": "Molecular Biologist & Computer Scientist 🧬👨🏻‍💻 Bioinformatics Developer at CRG", "uuid": 3199157 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 4.0", "role": "Depends" }, { "package": "shiny", "version": ">= 1.7.0", "role": "Depends" }, { "package": "shinyBS", "role": "Depends" }, { "package": "Rcpp", 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analyse principal components" ], "topics": [ "calculateLoadingsContribution" ] }, { "page": "colSums-EList-method", "title": "Sum columns using an 'EList-class' object", "topics": [ "colSums,EList-method" ] }, { "page": "convertGeneIdentifiers", "title": "Convert gene identifiers", "concept": [ "functions for gene expression pre-processing" ], "topics": [ "convertGeneIdentifiers" ] }, { "page": "correlateGEandAS", "title": "Correlate gene expression data against alternative splicing quantification", "concept": [ "functions to correlate gene expression and alternative splicing" ], "topics": [ "correlateGEandAS" ] }, { "page": "createGroupByAttribute", "title": "Split elements into groups based on a given column of a dataset", "concept": [ "functions for data grouping" ], "topics": [ "createGroupByAttribute" ] }, { "page": "diffAnalyses", "title": "Perform statistical analyses", "concept": [ "functions to perform and plot differential analyses" ], "topics": [ "diffAnalyses" ] }, { "page": "discardLowCoveragePSIvalues", "title": "Remove alternative splicing quantification values based on coverage", "topics": [ "discardLowCoveragePSIvalues" ] }, { "page": "ensemblToUniprot", "title": "Convert from Ensembl to UniProt identifier", "concept": [ "functions to retrieve external information" ], "topics": [ "ensemblToUniprot" ] }, { "page": "filterGeneExpr", "title": "Filter genes based on their expression", "concept": [ "functions for gene expression pre-processing" ], "topics": [ "filterGeneExpr" ] }, { "page": "filterGroups", "title": "Filter groups with less data points than the threshold", "topics": [ "filterGroups" ] }, { "page": "filterPSI", "title": "Filter alternative splicing quantification", "concept": [ "functions for PSI quantification" ], "topics": [ "filterPSI" ] }, { "page": "getAttributesTime", "title": "Get time values for given columns in a clinical dataset", "concept": [ "functions to analyse survival" ], "topics": [ "getAttributesTime" ] }, { "page": "getDownloadsFolder", "title": "Get the path to the Downloads folder", "concept": [ "functions associated with GTEx data retrieval", "functions associated with SRA data retrieval", "functions associated with TCGA data retrieval" ], "topics": [ "getDownloadsFolder" ] }, { "page": "getGeneList", "title": "Get curated, literature-based gene lists", "concept": [ "functions for data grouping" ], "topics": [ "getGeneList" ] }, { "page": "getGtexDataTypes", "title": "Get GTEx data information", "concept": [ "functions associated with GTEx data retrieval" ], "topics": [ "getGtexDataTypes", "getGtexReleases" ] }, { "page": "getGtexTissues", "title": "Get GTEx tissues from given GTEx sample attributes", "concept": [ "functions associated with GTEx data retrieval" ], "topics": [ "getGtexTissues" ] }, { "page": "getSampleFromSubject", "title": "Get samples matching the given subjects", "concept": [ "functions for data grouping" ], "topics": [ "getMatchingSamples", "getSampleFromPatient", 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"getTCGAdataTypes", "getTCGAdates" ] }, { "page": "groupPerElem", "title": "Assign one group to each element", "concept": [ "functions for data grouping" ], "topics": [ "groupPerElem" ] }, { "page": "isFirebrowseUp", "title": "Check if FireBrowse API is running", "concept": [ "functions associated with TCGA data retrieval" ], "topics": [ "isFirebrowseUp" ] }, { "page": "labelBasedOnCutoff", "title": "Label groups based on a given cutoff", "concept": [ "functions to analyse survival" ], "topics": [ "labelBasedOnCutoff" ] }, { "page": "listSplicingAnnotations", "title": "List alternative splicing annotations", "concept": [ "functions for PSI quantification" ], "topics": [ "listSplicingAnnotations" ] }, { "page": "loadAnnotation", "title": "Load alternative splicing annotation from 'AnnotationHub'", "concept": [ "functions for PSI quantification" ], "topics": [ "loadAnnotation" ] }, { "page": "loadGtexData", "title": "Download and load GTEx data", "concept": [ "functions associated with GTEx data retrieval", "functions to load data" ], "topics": [ "loadGtexData" ] }, { "page": "loadLocalFiles", "title": "Load local files", "concept": [ "functions to load data", "functions to load local files" ], "topics": [ "loadLocalFiles" ] }, { "page": "loadSRAproject", "title": "Download and load SRA projects via recount2", "concept": [ "functions associated with SRA data retrieval", "functions to load data" ], "topics": [ "loadSRAproject" ] }, { "page": "loadTCGAdata", "title": "Download and process TCGA data", "concept": [ "functions associated with TCGA data retrieval", "functions to load data" ], "topics": [ "loadFirebrowseData", "loadTCGAdata" ] }, { "page": "normaliseGeneExpression", "title": "Filter and normalise gene expression", "concept": [ "functions for gene expression pre-processing" ], "topics": [ "normaliseGeneExpression", "normalizeGeneExpression" ] }, { "page": "optimalSurvivalCutoff", "title": "Calculate optimal data cutoff that best separates survival curves", "concept": [ "functions to analyse survival" ], "topics": [ "optimalSurvivalCutoff" ] }, { "page": "parseCategoricalGroups", "title": "Parse categorical columns in a data frame", "topics": [ "parseCategoricalGroups" ] }, { "page": "parseSplicingEvent", "title": "Parse alternative splicing event identifier", "topics": [ "parseSplicingEvent" ] }, { "page": "parseMisoAnnotation", "title": "Parse events from alternative splicing annotation", "concept": [ "functions to prepare alternative splicing annotations" ], "topics": [ "parseMatsAnnotation", "parseMisoAnnotation", "parseSuppaAnnotation", "parseVastToolsAnnotation" ] }, { "page": "parseTCGAsampleInfo", "title": "Parse sample information from TCGA sample identifiers", "concept": [ "functions associated with TCGA data retrieval" ], "topics": [ "parseSampleGroups", "parseTCGAsampleInfo", "parseTcgaSampleInfo", "parseTCGAsampleTypes" ] }, { "page": "performICA", "title": "Perform independent component analysis after processing missing values", "concept": [ "functions to analyse independent components" ], "topics": [ "performICA" ] }, { "page": "performPCA", "title": "Perform principal component analysis after processing missing values", "concept": [ "functions to analyse principal components" ], "topics": [ "performPCA" ] }, { "page": "plotDistribution", "title": "Plot sample distribution", "concept": [ "functions to perform and plot differential analyses" ], "topics": [ "plotDistribution" ] }, { "page": "plotGeneExprPerSample", "title": "Plot distribution of gene expression per sample", "concept": [ "functions for gene expression pre-processing" ], "topics": [ "plotGeneExprPerSample" ] }, { "page": "plotGroupIndependence", "title": "Plot '-log10(p-values)' of the results obtained after multiple group independence testing", "concept": [ "functions for data grouping" ], "topics": [ "plotGroupIndependence" ] }, { "page": "plotICA", "title": "Create multiple scatterplots from ICA", "concept": [ "functions to analyse 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"processSurvTerms", "title": "Process survival curves terms to calculate survival curves", "concept": [ "functions to analyse survival" ], "topics": [ "processSurvTerms" ] }, { "page": "psichomics", "title": "Start graphical interface of psichomics", "topics": [ "psichomics" ] }, { "page": "quantifySplicing", "title": "Quantify alternative splicing events", "concept": [ "functions for PSI quantification" ], "topics": [ "quantifySplicing" ] }, { "page": "queryEnsemblByGene", "title": "Query information from Ensembl", "concept": [ "functions to retrieve external information" ], "topics": [ "queryEnsemblByEvent", "queryEnsemblByGene" ] }, { "page": "readFile", "title": "Load psichomics-specific file", "topics": [ "readFile" ] }, { "page": "survdiffTerms", "title": "Test Survival Curve Differences", "concept": [ "functions to analyse survival" ], "topics": [ "survdiffTerms" ] }, { "page": "survfit.survTerms", "title": "Create survival curves", "concept": [ "functions to analyse survival" 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