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Merge pull request #250 from morinlab/kdreval-gamblr-verse
Transforming GAMBLR to a universe
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,155 +1,2 @@ | ||
| # Generated by roxygen2: do not edit by hand | ||
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| export(FtestCNV) | ||
| export(adjust_ploidy) | ||
| export(annotate_driver_ssm) | ||
| export(annotate_hotspots) | ||
| export(annotate_igh_breakpoints) | ||
| export(annotate_maf_triplet) | ||
| export(annotate_ssm_blacklist) | ||
| export(annotate_ssm_motif_context) | ||
| export(annotate_sv) | ||
| export(ashm_multi_rainbow_plot) | ||
| export(ashm_rainbow_plot) | ||
| export(assemble_file_details) | ||
| export(assign_cn_to_ssm) | ||
| export(calc_mutation_frequency_bin_region) | ||
| export(calc_mutation_frequency_bin_regions) | ||
| export(calculate_pga) | ||
| export(check_gambl_metadata) | ||
| export(check_gamblr_config) | ||
| export(check_host) | ||
| export(check_remote_configuration) | ||
| export(cleanup_maf) | ||
| export(cnvKompare) | ||
| export(collate_lymphgen) | ||
| export(collate_results) | ||
| export(comp_report) | ||
| export(consolidate_lymphgen) | ||
| export(copy_number_vaf_plot) | ||
| export(count_ssm_by_region) | ||
| export(custom_caselist) | ||
| export(estimate_purity) | ||
| export(fancy_alignment_plot) | ||
| export(fancy_circos_plot) | ||
| export(fancy_cnbar) | ||
| export(fancy_ideogram) | ||
| export(fancy_multisamp_ideogram) | ||
| export(fancy_propcov_plot) | ||
| export(fancy_proportions_plot) | ||
| export(fancy_qc_plot) | ||
| export(fancy_snv_chrdistplot) | ||
| export(fancy_sv_sizedens) | ||
| export(fancy_v_chrcount) | ||
| export(fancy_v_count) | ||
| export(fancy_v_sizedis) | ||
| export(fetch_output_files) | ||
| export(finalize_study) | ||
| export(find_expected_outputs) | ||
| export(find_files_extract_wildcards) | ||
| export(focal_cn_plot) | ||
| export(fread_maf) | ||
| export(gene_to_region) | ||
| export(genome_to_exome) | ||
| export(get_ashm_count_matrix) | ||
| export(get_bams) | ||
| export(get_cn_segments) | ||
| export(get_cn_states) | ||
| export(get_cnv_and_ssm_status) | ||
| export(get_coding_ssm) | ||
| export(get_coding_ssm_status) | ||
| export(get_combined_sv) | ||
| export(get_excluded_samples) | ||
| export(get_gambl_colours) | ||
| export(get_gambl_metadata) | ||
| export(get_gene_cn_and_expression) | ||
| export(get_gene_expression) | ||
| export(get_lymphgen) | ||
| export(get_manta_sv) | ||
| export(get_manta_sv_by_sample) | ||
| export(get_manta_sv_by_samples) | ||
| export(get_sample_cn_segments) | ||
| export(get_sample_wildcards) | ||
| export(get_samples_md5_hash) | ||
| export(get_ssh_session) | ||
| export(get_ssm_by_patients) | ||
| export(get_ssm_by_region) | ||
| export(get_ssm_by_regions) | ||
| export(get_ssm_by_sample) | ||
| export(get_ssm_by_samples) | ||
| export(get_study_info) | ||
| export(heatmap_mutation_frequency_bin) | ||
| export(intersect_maf) | ||
| export(liftover_bedpe) | ||
| export(maf_to_custom_track) | ||
| export(make_igv_snapshot) | ||
| export(plot_sample_circos) | ||
| export(populate_each_tool_result) | ||
| export(prettyChromoplot) | ||
| export(prettyCoOncoplot) | ||
| export(prettyForestPlot) | ||
| export(prettyGeneCloud) | ||
| export(prettyOncoplot) | ||
| export(prettyRainfallPlot) | ||
| export(pretty_lollipop_plot) | ||
| export(region_to_bins) | ||
| export(region_to_gene) | ||
| export(review_hotspots) | ||
| export(sanitize_maf_data) | ||
| export(setup_expreession_data) | ||
| export(setup_fusions) | ||
| export(setup_study) | ||
| export(splendidHeatmap) | ||
| export(study_check) | ||
| export(supplement_maf) | ||
| export(sv_to_bedpe_file) | ||
| export(sv_to_custom_track) | ||
| export(theme_Morons) | ||
| export(tidy_gene_expression) | ||
| export(tidy_lymphgen) | ||
| export(view_mutation_igv) | ||
| export(write_sample_set_hash) | ||
| import(ComplexHeatmap) | ||
| import(DBI) | ||
| import(GAMBLR.data) | ||
| import(GenomicRanges, except = c("merge", "shift", "union", "intersect", "setdiff", "reduce")) | ||
| import(IRanges, except = c("merge", "shift", "collapse", "union", "slice", "intersect", "setdiff", "desc", "reduce")) | ||
| import(RCircos) | ||
| import(RColorBrewer) | ||
| import(RMariaDB) | ||
| import(Rsamtools) | ||
| import(S4Vectors, except = c("merge", "second", "first", "union", "intersect", "setdiff", "setequal", "rename", "expand")) | ||
| import(SRAdb) | ||
| import(broom) | ||
| import(circlize) | ||
| import(config) | ||
| import(cowplot) | ||
| import(data.table, except = c("last", "first", "between", "transpose")) | ||
| import(digest) | ||
| import(dplyr) | ||
| import(forcats) | ||
| import(g3viz) | ||
| import(ggbeeswarm) | ||
| import(ggplot2) | ||
| import(ggpubr, except = "get_legend") | ||
| import(ggrepel) | ||
| import(ggsci) | ||
| import(grid) | ||
| import(gridExtra, except = "combine") | ||
| import(maftools) | ||
| import(metaviz) | ||
| import(plotly, except = c("last_plot", "add_heatmap", "export")) | ||
| import(purrr) | ||
| import(readr) | ||
| import(rtracklayer) | ||
| import(ssh) | ||
| import(stringi) | ||
| import(stringr) | ||
| import(tibble) | ||
| import(tidyr) | ||
| import(vroom, except = c("col_skip", "fwf_positions", "default_locale", "date_names_lang", "cols_only", "output_column", "col_character", "col_guess", "spec", "as.col_spec", "fwf_cols", "cols", "col_date", "col_datetime", "locale", "col_time", "cols_condense", "col_logical", "col_number", "col_integer", "col_factor", "fwf_widths", "date_names_langs", "problems", "date_names", "col_double", "fwf_empty")) | ||
| import(wordcloud) | ||
| import(workflowr) | ||
| importFrom(ggthemes,theme_foundation) | ||
| importFrom(plyr,round_any) | ||
| importFrom(utils,getFromNamespace) |
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