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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export(add_icgc_metadata)
export(annotate_hotspots)
export(annotate_maf_triplet)
export(annotate_ssm_blacklist)
export(annotate_ssm_motif_context)
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(cbio_custom_caselist)
export(cbio_finalize_study)
export(cbio_setup_expreession_data)
export(cbio_setup_fusions)
export(cbio_setup_study)
export(cbio_study_check)
export(check_gambl_metadata)
export(check_gamblr_config)
export(check_gene_expression)
export(check_host)
export(check_remote_configuration)
export(cleanup_maf)
export(collate_lymphgen)
export(collate_results)
export(consolidate_lymphgen)
export(estimate_purity)
export(fetch_output_files)
export(find_expected_outputs)
export(find_files_extract_wildcards)
export(get_all_coding_ssm)
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_metadata)
export(get_gambl_outcomes)
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_raw_expression_counts)
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_regions)
export(get_ssm_by_samples)
export(get_study_info)
export(id_ease)
export(link_seq_types)
export(og_get_gambl_metadata)
export(populate_each_tool_result)
export(pretty_lymphoplot)
export(tidy_gene_expression)
export(write_sample_set_hash)
import(BSgenome)
import(ComplexHeatmap)
import(DBI)
import(GAMBLR.data)
import(GAMBLR.helpers)
import(GAMBLR.utils)
import(GenomicDistributions)
import(GenomicRanges, except = c("start", "end", "merge", "shift", "union", "intersect", "setdiff", "reduce", "trim"))
import(IRanges, except = c("start", "end", "merge", "shift", "collapse", "union", "slice", "intersect", "setdiff", "desc", "reduce", "trim"))
import(RMariaDB)
import(Rsamtools)
import(circlize)
import(config)
import(data.table, except = c("last", "first", "between", "transpose"))
import(digest)
import(dplyr)
import(ggplot2)
import(ggsci)
import(glue)
import(grid)
import(msigdbr)
import(org.Hs.eg.db)
import(purrr)
import(readr)
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"))
importFrom(GAMBLR.helpers,check_config_value)
importFrom(GAMBLR.helpers,maf_header)
importFrom(GAMBLR.utils,fread_maf)
importFrom(GAMBLR.utils,tidy_lymphgen)
importFrom(utils,read.table)