Package: psichomics
Title: Graphical Interface for Alternative Splicing Quantification, Analysis and
    Visualisation
Version: 1.37.0
Encoding: UTF-8
Authors@R: c(
        person("Nuno", "Saraiva-Agostinho",
               email="nunodanielagostinho@gmail.com", role=c("aut", "cre"),
               comment=c(ORCID="0000-0002-5549-105X")),
        person(c("Nuno", "Luís"), "Barbosa-Morais", role=c("aut", "led", "ths"),
               comment=c(ORCID="0000-0002-1215-0538")),
        person("André", "Falcão", role="ths"), 
        person("Lina", "Gallego Paez", role="ctb"), 
        person("Marie", "Bordone", role="ctb"), 
        person("Teresa", "Maia", role="ctb"),
        person("Mariana", "Ferreira", role="ctb"),
        person("Ana Carolina", "Leote", role="ctb"), 
        person("Bernardo", "de Almeida", role="ctb"))
Description: 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.
Depends:
    R (>= 4.0),
    shiny (>= 1.7.0),
    shinyBS
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 7.3.1
Imports:
    AnnotationDbi,
    AnnotationHub,
    BiocFileCache,
    cluster,
    colourpicker,
    data.table,
    digest,
    dplyr,
    DT (>= 0.2),
    edgeR,
    fastICA,
    fastmatch,
    ggplot2,
    ggrepel,
    graphics,
    grDevices,
    highcharter (>= 0.5.0),
    htmltools,
    httr,
    jsonlite,
    limma,
    pairsD3,
    plyr,
    purrr,
    Rcpp (>= 0.12.14),
    recount,
    Rfast,
    R.utils,
    reshape2,
    shinyjs,
    stringr,
    stats,
    SummarizedExperiment,
    survival,
    tools,
    utils,
    XML,
    xtable,
    methods
Suggests:
    testthat,
    knitr,
    parallel,
    devtools,
    rmarkdown,
    gplots,
    covr,
    car,
    rstudioapi,
    spelling
LinkingTo: Rcpp
VignetteBuilder: knitr
Collate: 
    'RcppExports.R'
    'utils.R'
    'globalAccess.R'
    'app.R'
    'analysis.R'
    'analysis_correlation.R'
    'analysis_diffExpression.R'
    'analysis_diffExpression_event.R'
    'analysis_diffExpression_table.R'
    'analysis_diffSplicing.R'
    'analysis_diffSplicing_event.R'
    'analysis_diffSplicing_table.R'
    'analysis_dimReduction.R'
    'analysis_dimReduction_ica.R'
    'analysis_dimReduction_pca.R'
    'analysis_information.R'
    'analysis_survival.R'
    'analysis_template.R'
    'data.R'
    'formats.R'
    'data_firebrowse.R'
    'data_geNormalisationFiltering.R'
    'data_gtex.R'
    'data_inclusionLevels.R'
    'data_inclusionLevelsFilter.R'
    'data_local.R'
    'data_recount.R'
    'events_suppa.R'
    'events_vastTools.R'
    'events_miso.R'
    'events_mats.R'
    'events.R'
    'formats_SraRunTableSampleInfo.R'
    'formats_firebrowseGeneExpression.R'
    'formats_firebrowseJunctionReads.R'
    'formats_firebrowseMergeClinical.R'
    'formats_firebrowseNormalizedGeneExpression.R'
    'formats_genericClinical.R'
    'formats_genericGeneExpression.R'
    'formats_genericInclusionLevels.R'
    'formats_genericJunctionReads.R'
    'formats_genericSampleInfo.R'
    'formats_gtexClinical.R'
    'formats_gtexGeneReadsFormat.R'
    'formats_gtexJunctionReads.R'
    'formats_gtexSampleInfo.R'
    'formats_gtexV7Clinical.R'
    'formats_gtexV7JunctionReads.R'
    'formats_gtexV8JunctionReads.R'
    'formats_psichomicsGeneExpression.R'
    'formats_psichomicsInclusionLevels.R'
    'formats_recountSampleInfo.R'
    'formats_vasttoolsGeneExpression.R'
    'formats_vasttoolsInclusionLevels.R'
    'formats_vasttoolsInclusionLevelsTidy.R'
    'groups.R'
    'help.R'
    'utils_drawSplicingEvent.R'
    'utils_eventParsing.R'
    'utils_fileBrowserDialog.R'
    'utils_interactiveGgplot.R'
    'utils_interface.R'
biocViews: Sequencing, RNASeq, AlternativeSplicing,
    DifferentialSplicing, Transcription, GUI, PrincipalComponent,
    Survival, BiomedicalInformatics, Transcriptomics, ImmunoOncology,
    Visualization, MultipleComparison, GeneExpression, DifferentialExpression
URL: https://nuno-agostinho.github.io/psichomics/,
    https://github.com/nuno-agostinho/psichomics/
BugReports: https://github.com/nuno-agostinho/psichomics/issues
Language: en-GB
git_url: https://git.bioconductor.org/packages/psichomics
git_branch: devel
git_last_commit: a7c8792
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
