Package: genoppi
Title: genoppi
Version: 1.0.0
Authors@R: 
    c(person(given = "Frederik",
             family = "Lassen",
             role = c("aut", "cre"),
             email = "flassen@broadinstitute.org"),
      person(given = "Yu-Han",
             family = "Hsu",
             role = c("aut"),
             email = "yuhanhsu@broadinstitute.org"))
Description: An open-source software for robust and standardized integration of proteomic and genetic data.
License: MIT + file LICENSE
LazyData: true
Depends:
    R (>= 3.6),
    hash,
    ggplot2,
    shiny,
    shinydashboard,
    plotly,
Suggests:
    devtools,
    covr,
    grid,
    png,
    testthat (>= 2.1.0)
Imports:
    stats,
    ggrepel,
    shinyjs,
    data.table,
    RColorBrewer,
    VennDiagram,
    colourpicker,
    futile.logger,
    shinycssloaders,
    DT,
    limma,
Encoding: UTF-8
RoxygenNote: 7.1.1
Collate: 
    'add_plotly_layout_scatter.R'
    'add_plotly_layout_volcano.R'
    'add_plotly_line_unity.R'
    'add_plotly_markers_search.R'
    'add_plotly_markers_search_pathway.R'
    'add_plotly_threshold_lines.R'
    'add_plotly_trace.R'
    'append_to_column.R'
    'calc_cumsum_table.R'
    'calc_fisher.R'
    'calc_hyper.R'
    'calc_logfc_limit.R'
    'calc_mod_ttest.R'
    'check_input.R'
    'collapse_labels.R'
    'data.R'
    'draw_genoppi_venn.R'
    'enumerate_replicate_combinations.R'
    'get_geneset_overlay.R'
    'get_gene_from_snp.R'
    'get_gene_lists.R'
    'get_gwas_lists.R'
    'get_bioplex_list.R'
    'get_inweb_list.R'
    'get_irefindex_list.R'
    'get_overlay_df.R'
    'get_pathways.R'
    'get_replicate_summary_text.R'
    'get_shiny_errors.R'
    'get_snp_lists.R'
    'get_tissue_lists.R'
    'html_translate_significance_thresholds.R'
    'id_enriched_proteins.R'
    'lapply_calc_hyper.R'
    'launch_genoppi.R'
    'make_interactive.R'
    'map_gene_id.R'
    'misc.R'
    'parse_uploaded_file.R'
    'parse_rd.R'
    'plot_overlay.R'
    'plot_scatter_basic.R'
    'plot_tissue_enrichment.R'
    'plot_volcano_basic.R'
    'read_input.R'
    'set_names_by_dataset.R'
    'stop_invalid.R'
    'subset_snp_loci.R'
    'tabulate_markers.R'
    'theme_genoppi.R'
    'to_overlay_data.R'
    'validate_reference.R'
    'venn_to_table.R'
biocViews: limma
