Package: psichomics
Title: Graphical Interface for Alternative Splicing Quantification,
        Analysis and Visualisation
Version: 1.4.5
Encoding: UTF-8
Authors@R: c( person("Nuno", "Saraiva-Agostinho", ,
        "nunodanielagostinho@gmail.com", role = c("aut", "cre")),
        person(c("Nuno", "Luís"), "Barbosa-Morais",
        role=c("aut", "led", "ths")),
        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 from large transcriptomic 
    datasets, including those from The Cancer Genome Atlas (TCGA) and the 
    Genotype-Tissue Expression project (GTEx), as well as user-owned 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 (>= 3.4), shiny (>= 1.0.3), shinyBS
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 6.0.1
Imports: AnnotationHub, cluster, colourpicker, data.table, digest,
        dplyr, DT (>= 0.2), edgeR, fastICA, fastmatch, ggplot2,
        ggrepel, grDevices, highcharter (>= 0.5.0), htmltools, httr,
        jsonlite, limma, miscTools, pairsD3, plyr, Rcpp (>= 0.12.14),
        R.utils, shinyjs, stringr, stats, survival, tools, utils, XML,
        xtable, methods
Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
        car
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_local.R' 'events_suppa.R'
        'events_vastTools.R' 'events_miso.R' 'events_mats.R' 'events.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_psichomicsGeneExpression.R'
        'formats_psichomicsInclusionLevels.R' 'groups.R' 'help.R'
biocViews: Sequencing, RNASeq, AlternativeSplicing,
        DifferentialSplicing, Transcription, GUI, PrincipalComponent,
        Survival, BiomedicalInformatics, Transcriptomics,
        Visualization, MultipleComparison, GeneExpression,
        DifferentialExpression
URL: https://github.com/nuno-agostinho/psichomics
BugReports: https://github.com/nuno-agostinho/psichomics/issues
NeedsCompilation: yes
Packaged: 2018-04-05 01:31:53 UTC; biocbuild
Author: 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]
Maintainer: Nuno Saraiva-Agostinho <nunodanielagostinho@gmail.com>
Built: R 3.4.4; i386-w64-mingw32; 2018-04-05 06:25:54 UTC; windows
Archs: i386, x64
