Package: psichomics
Title: Graphical Interface for Alternative Splicing Quantification,
        Analysis and Visualisation
Version: 1.34.0
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
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: RELEASE_3_21
git_last_commit: 1e06f30
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-16 03:01:35 UTC; biocbuild
Author: Nuno Saraiva-Agostinho [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-5549-105X>),
  Nuno Luís Barbosa-Morais [aut, led, ths] (ORCID:
    <https://orcid.org/0000-0002-1215-0538>),
  André Falcão [ths],
  Lina Gallego Paez [ctb],
  Marie Bordone [ctb],
  Teresa Maia [ctb],
  Mariana Ferreira [ctb],
  Ana Carolina Leote [ctb],
  Bernardo de Almeida [ctb]
Maintainer: Nuno Saraiva-Agostinho <nunodanielagostinho@gmail.com>
Built: R 4.5.0; x86_64-w64-mingw32; 2025-04-16 15:14:01 UTC; windows
Archs: x64
