Package: psichomics
Title: Graphical Interface for Alternative Splicing Quantification,
        Analysis and Visualisation
Version: 1.0.8
Encoding: UTF-8
Authors@R: c( person("Nuno", "Saraiva-Agostinho", ,
        "nunodanielagostinho@gmail.com", role = c("aut", "cre")),
        person("Nuno", "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", "Almeida", role="ctb"))
Description: Package with a Shiny-based graphical interface for the integrated
    analysis of alternative splicing data from The Cancer Genome Atlas (TCGA).
    This tool interactively performs survival, principal components and
    differential splicing analyses with direct incorporation of clinical
    features (such as tumour stage or survival) associated with TCGA samples.
Depends: R (>= 3.3), shiny (>= 1.0.0), shinyBS
License: MIT + file LICENSE
LazyData: true
RoxygenNote: 6.0.1
Imports: AnnotationHub, data.table, digest, dplyr, DT (>= 0.2),
        fastmatch, highcharter (>= 0.5.0), httr, jsonlite, miscTools,
        plyr, R.utils, shinyjs, stringr, stats, survival, Sushi, tools,
        utils, XML, methods
Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr,
        car
VignetteBuilder: knitr
Collate: 'analysis.R' 'analysis_diffSplicing.R'
        'analysis_diffSplicing_event.R' 'analysis_diffSplicing_table.R'
        'analysis_information.R' 'analysis_pca.R' 'analysis_survival.R'
        'analysis_template.R' 'utils.R' 'globalAccess.R' 'app.R'
        'data.R' 'formats.R' 'data_firebrowse.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_firehoseGeneExpression.R'
        'formats_firehoseJunctionReads.R'
        'formats_firehoseMergeClinical.R' 'formats_gtexClinical.R'
        'formats_gtexJunctionReads.R' 'formats_gtexSampleInfo.R'
        'groups.R' 'settings.R'
biocViews: Sequencing, RNASeq, AlternativeSplicing,
        DifferentialSplicing, Transcription, GUI, PrincipalComponent,
        Survival, BiomedicalInformatics, Transcriptomics,
        Visualization, MultipleComparison
URL: https://github.com/nuno-agostinho/psichomics
BugReports: https://github.com/nuno-agostinho/psichomics/issues
NeedsCompilation: no
Packaged: 2017-02-22 01:40:42 UTC; biocbuild
Author: Nuno Saraiva-Agostinho [aut, cre],
  Nuno Barbosa-Morais [aut, ths],
  André Falcão [ths],
  Lina Gallego Paez [ctb],
  Marie Bordone [ctb],
  Teresa Maia [ctb],
  Mariana Ferreira [ctb],
  Ana Carolina Leote [ctb],
  Bernardo Almeida [ctb]
Maintainer: Nuno Saraiva-Agostinho <nunodanielagostinho@gmail.com>
Built: R 3.3.2; ; 2017-02-22 05:16:26 UTC; windows
