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 |