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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(get_analysis_status,combined.quality.metrics.output)
S3method(get_dna_expanded_metrics,combined.quality.metrics.output)
S3method(get_dna_qc_metrics,combined.quality.metrics.output)
S3method(get_dna_qc_metrics_cnv,combined.quality.metrics.output)
S3method(get_dna_qc_metrics_msi,combined.quality.metrics.output)
S3method(get_dna_qc_metrics_snvtmb,combined.quality.metrics.output)
S3method(get_fusions,combined.variant.output)
S3method(get_gene_amplifications,combined.variant.output)
S3method(get_rna_expanded_metrics,combined.quality.metrics.output)
S3method(get_rna_qc_metrics,combined.quality.metrics.output)
S3method(get_run_qc_metrics,combined.quality.metrics.output)
S3method(get_small_variants,combined.variant.output)
S3method(get_splice_variants,combined.variant.output)
export(add_amplification_data)
export(add_annotation_data)
export(add_common_theme_elements)
export(add_tmb_variant_data)
export(cnv)
export(cvo)
export(filter_consequences)
export(filter_depth)
export(filter_for_Included_in_TMB)
export(filter_for_cosmic_id)
export(filter_germline_db)
export(filter_germline_proxi)
export(generate_dragen_samplesheet)
export(get_analysis_details_df)
export(get_analysis_status)
export(get_count_df)
export(get_dna_expanded_metrics)
export(get_dna_qc_metrics)
export(get_dna_qc_metrics_cnv)
export(get_dna_qc_metrics_msi)
export(get_dna_qc_metrics_snvtmb)
export(get_fusions)
export(get_gene_amplifications)
export(get_metrics_df)
export(get_rna_expanded_metrics)
export(get_rna_qc_metrics)
export(get_run_qc_metrics)
export(get_sequencing_run_details_df)
export(get_small_variants)
export(get_splice_variants)
export(keep_consequences)
export(make_qc_table)
export(parse_p_dot_notation)
export(plot_af_density)
export(plot_af_histogram)
export(plot_af_per_variant_consequence)
export(plot_onco_print)
export(prepare_dataframe_for_oncoprint)
export(process_and_filter_small_variant_data)
export(qualitymetrics)
export(read_analysis_status)
export(read_annotation_data)
export(read_cnv_data)
export(read_cvo_data)
export(read_dna_expanded_metrics)
export(read_dna_qc_metrics)
export(read_dna_qc_metrics_cnv)
export(read_dna_qc_metrics_msi)
export(read_dna_qc_metrics_snvtmb)
export(read_fusions)
export(read_gene_amplifications)
export(read_qmo_data)
export(read_rna_expanded_metrics)
export(read_rna_qc_metrics)
export(read_run_qc_metrics)
export(read_small_variants)
export(read_splice_variants)
export(read_tmb_details_data)
export(read_tmb_details_data_csv)
export(read_tmb_trace_data)
export(summarize_cnv_data)
export(tmb)
export(write_multiqc_data)
export(write_rdata_file)
export(write_workbook)
importFrom(dplyr,bind_rows)
importFrom(dplyr,case_when)
importFrom(dplyr,distinct)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(stringr,str_split_i)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(vcfR,read.vcfR)
importFrom(vcfR,vcfR2tidy)