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| add_h_arrow | Add Horizontal Arrow with Text Label to a ggplot |
| add_labels | Add Text Labels to a ggplot |
| centromeres.hg19 | Location of Centromeres at Genome Build hg19 |
| centromeres.hg38 | Location of Centromeres at Genome Build hg38 |
| chromsize.hg19 | Chromosome Size of Genome Build hg19 |
| chromsize.hg38 | Chromosome Size of Genome Build hg38 |
| CN.features | Classfication Table of Copy Number Features Devised by Wang et al. |
| CopyNumber | Class CopyNumber |
| CopyNumber-class | Class CopyNumber |
| cytobands.hg19 | Location of Chromosome Cytobands at Genome Build hg19 |
| cytobands.hg38 | Location of Chromosome Cytobands at Genome Build hg38 |
| enrich_component_strand_bias | Performs Strand Bias Enrichment Analysis for a Given Sample-by-Component Matrix |
| get_adj_p | Get Adjust P Values from Group Comparison |
| get_bayesian_result | Get Specified Bayesian NMF Result from Run |
| get_cn_ploidy | Get Ploidy from Absolute Copy Number Profile |
| get_genome_annotation | Get Genome Annotation |
| get_groups | Get Sample Groups from Signature Decomposition Information |
| get_group_comparison | Get Comparison Result between Signature Groups |
| get_sig_exposure | Get Signature Exposure from 'Signature' Object |
| get_sig_feature_association | Calculate Association between Signature Exposures and Other Features |
| get_sig_similarity | Calculate Similarity between Identified Signatures and Reference Signatures |
| get_tidy_association | Get Tidy Signature Association Results |
| get_tidy_parameter | Get Tidy Parameter from Flexmix Model |
| handle_hyper_mutation | Handle Hypermutant Samples |
| hello | Say Hello to Users |
| MAF | Class MAF |
| MAF-class | Class MAF |
| read_copynumber | Read Absolute Copy Number Profile |
| read_maf | Read MAF Files |
| report_bootstrap_p_value | Report P Values from bootstrap Results |
| scoring | Score Copy Number Profile |
| show_catalogue | Show Alteration Catalogue Profile |
| show_cn_circos | Show Copy Number Profile in Circos |
| show_cn_components | Show Copy Number Components |
| show_cn_distribution | Show Copy Number Distribution either by Length or Chromosome |
| show_cn_features | Show Copy Number Feature Distributions |
| show_cn_profile | Show Sample Copy Number Profile |
| show_cosmic_sig_profile | Plot COSMIC Signature Profile |
| show_groups | Show Signature Contribution in Clusters |
| show_group_comparison | Plot Group Comparison Result |
| show_group_mapping | Map Groups using Sankey |
| show_sig_bootstrap | Show Signature Bootstrap Analysis Results |
| show_sig_bootstrap_error | Show Signature Bootstrap Analysis Results |
| show_sig_bootstrap_exposure | Show Signature Bootstrap Analysis Results |
| show_sig_bootstrap_stability | Show Signature Bootstrap Analysis Results |
| show_sig_consensusmap | Show Signature Consensus Map |
| show_sig_exposure | Plot Signature Exposure |
| show_sig_feature_corrplot | Draw Corrplot for Signature Exposures and Other Features |
| show_sig_fit | Show Signature Fit Result |
| show_sig_number_survey | Show Simplified Signature Number Survey |
| show_sig_number_survey2 | Show Comprehensive Signature Number Survey |
| show_sig_profile | Show Signature Profile |
| sigminer | sigminer: Extract, Analyze and Visualize Signatures for Genomic Variations |
| sig_attrs | Obtain or Modify Signature Information |
| sig_auto_extract | Extract Signatures through the Automatic Relevance Determination Technique |
| sig_convert | Convert Signatures between different Genomic Distribution of Components |
| sig_estimate | Estimate Signature Number |
| sig_exposure | Obtain or Modify Signature Information |
| sig_extract | Extract Signatures through NMF |
| sig_fit | Fit Signature Exposures with Linear Combination Decomposition |
| sig_fit_bootstrap | Obtain Bootstrap Distribution of Signature Exposures of a Certain Tumor Sample |
| sig_fit_bootstrap_batch | Exposure Instability Analysis of Signature Exposures with Bootstrapping |
| sig_modify_names | Obtain or Modify Signature Information |
| sig_names | Obtain or Modify Signature Information |
| sig_number | Obtain or Modify Signature Information |
| sig_signature | Obtain or Modify Signature Information |
| sig_tally | Tally a Genomic Alteration Object |
| sig_tally.CopyNumber | Tally a Genomic Alteration Object |
| sig_tally.MAF | Tally a Genomic Alteration Object |
| subset.CopyNumber | Subsetting CopyNumber object |
| transcript.hg19 | Merged Transcript Location at Genome Build hg19 |
| transcript.hg38 | Merged Transcript Location at Genome Build hg38 |
| use_color_style | Set Color Style for Plotting |