Function reference
CHORD
Functions related to CHORD (https://github.com/UMCUGenetics/CHORD)
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chord_mantavcf2df() - Convert Manta VCF to data.frame
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chord_run() - Run CHORD
HRDetect
Functions related to HRDetect (https://github.com/Nik-Zainal-Group/signature.tools.lib)
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hrdetect_prep_cnv() - Prepare PURPLE Somatic CNVs for HRDetect
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hrdetect_prep_snvindel() - Prepare VCF with SNVs/INDELs for use with HRDetect
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hrdetect_prep_sv() - Prepare VCF with SVs for use with HRDetect
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hrdetect_read_purple_cnv() - Read PURPLE Somatic CNVs for HRDetect
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hrdetect_read_snvindel_vcf() - Read VCF with SNVs/INDELs for use with HRDetect
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hrdetect_read_sv_vcf() - Read VCF with SVs for use with HRDetect
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hrdetect_run() - Run HRDetect via signature.tools.lib
MutationalPatterns
Functions related to MutationalPatterns (https://github.com/UMCUGenetics/MutationalPatterns)
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cosmic_signatures_2015 - Get COSMIC 2015 Signatures
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sig_contribution() - Calculate COSMIC Signature Contribution
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sig_contribution_table() - Create COSMIC Signature Table
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sig_count_dbs() - Count DBS Contexts
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sig_count_indel() - Count INDEL Contexts
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sig_count_snv() - Count SNV Contexts
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sig_plot_dbs() - Plot DBS Mutation Characteristics
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sig_plot_indel() - Plot INDEL Mutation Characteristics
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sig_plot_snv() - Plot SNV Mutation Characteristics
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sig_workflow_run() - Run MutationalPatterns Workflow
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get_genome_obj() - Get BSgenome Object