{ "_id": "6a2127aacd65a98ecbd217cc", "Package": "sigminer", "Title": "Extract, Analyze and Visualize Mutational Signatures for Genomic\nVariations", "Version": "2.3.2.9000", "Authors@R": "c(\nperson(\"Shixiang\", \"Wang\", , \"w_shixiang@163.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-9855-7357\")),\nperson(\"Ziyu\", \"Tao\", , \"taozy@shanghaitech.edu.cn\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-3272-1227\")),\nperson(\"Huimin\", \"Li\", , \"lihm@shanghaitech.edu.cn\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-1683-9057\")),\nperson(\"Tao\", \"Wu\", , \"wutao2@shanghaitech.edu.cn\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8999-9628\")),\nperson(\"Xue-Song\", \"Liu\", role = c(\"aut\", \"ctb\"),\ncomment = c(ORCID = \"0000-0002-7736-0077\")),\nperson(\"Anand\", \"Mayakonda\", role = \"ctb\")\n)", "Description": "Genomic alterations including single nucleotide\nsubstitution, copy number alteration, etc. are the major force\nfor cancer initialization and development. Due to the\nspecificity of molecular lesions caused by genomic alterations,\nwe can generate characteristic alteration spectra, called\n'signature' (Wang, Shixiang, et al. (2021)\n & Alexandrov, Ludmil B., et\nal. (2020) & Steele Christopher\nD., et al. (2022) ). This\npackage helps users to extract, analyze and visualize\nsignatures from genomic alteration records, thus providing new\ninsight into cancer study.", "License": "MIT + file LICENSE", "URL": "https://github.com/ShixiangWang/sigminer,\nhttps://shixiangwang.github.io/sigminer/,\nhttps://shixiangwang.github.io/sigminer-book/", "BugReports": "https://github.com/ShixiangWang/sigminer/issues", "VignetteBuilder": "knitr", "biocViews": "", "Encoding": "UTF-8", "LazyData": "true", "Roxygen": "list(markdown = TRUE, roclets = c(\"collate\", \"namespace\",\n\"rd\", \"roxytest::testthat_roclet\"))", "RoxygenNote": "7.3.2", "Config/testthat/edition": "3", "Config/pak/sysreqs": "cmake make libbz2-dev libicu-dev liblzma-dev\nxz-utils zlib1g-dev", "Repository": "https://shixiangwang.r-universe.dev", "Date/Publication": "2025-12-25 15:31:42 UTC", "RemoteUrl": "https://github.com/ShixiangWang/sigminer", "RemoteRef": "HEAD", "RemoteSha": "94be27b1714c1e3cc71e453334dff664646d64bd", "NeedsCompilation": 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Build mm10", "topics": [ "cytobands.mm10" ] }, { "page": "cytobands.mm9", "title": "Location of Chromosome Cytobands at Genome Build mm9", "topics": [ "cytobands.mm9" ] }, { "page": "cytobands.T2T", "title": "Location of Chromosome Cytobands at Genome Build T2T", "topics": [ "cytobands.T2T" ] }, { "page": "enrich_component_strand_bias", "title": "Performs Strand Bias Enrichment Analysis for a Given Sample-by-Component Matrix", "topics": [ "enrich_component_strand_bias" ] }, { "page": "get_adj_p", "title": "Get Adjust P Values from Group Comparison", "topics": [ "get_adj_p" ] }, { "page": "get_Aneuploidy_score", "title": "Get Aneuploidy Score from Copy Number Profile", "topics": [ "get_Aneuploidy_score" ] }, { "page": "get_bayesian_result", "title": "Get Specified Bayesian NMF Result from Run", "topics": [ "get_bayesian_result" ] }, { "page": "get_cn_freq_table", "title": "Get CNV Frequency Table", "topics": [ "get_cn_freq_table" ] }, { "page": "get_cn_ploidy", "title": "Get Ploidy from Absolute Copy Number Profile", "topics": [ "get_cn_ploidy" ] }, { "page": "get_genome_annotation", "title": "Get Genome Annotation", "topics": [ "get_genome_annotation" ] }, { "page": "get_group_comparison", "title": "Get Comparison Result between Signature Groups", "topics": [ "get_group_comparison" ] }, { "page": "get_groups", "title": "Get Sample Groups from Signature Decomposition Information", "topics": [ "get_groups" ] }, { "page": "get_intersect_size", "title": "Get Overlap Size between Interval x and y", "topics": [ "get_intersect_size" ] }, { "page": "get_pLOH_score", "title": "Get proportions of pLOH score from Allele Specific Copy Number Profile", "topics": [ "get_pLOH_score" ] }, { "page": "get_shannon_diversity_index", "title": "Get Shannon Diversity Index for Signatures", "topics": [ "get_shannon_diversity_index" ] }, { "page": "get_sig_cancer_type_index", "title": "Obtain Signature Index for Cancer Types", "topics": [ "get_sig_cancer_type_index" ] }, { "page": "get_sig_db", "title": "Get Curated Reference Signature Database", "topics": [ "get_sig_db" ] }, { "page": "get_sig_exposure", "title": "Get Signature Exposure from 'Signature' Object", "topics": [ "get_sig_exposure" ] }, { "page": "get_sig_feature_association", "title": "Calculate Association between Signature Exposures and Other Features", "topics": [ "get_sig_feature_association" ] }, { "page": "get_sig_rec_similarity", "title": "Get Reconstructed Profile Cosine Similarity, RSS, etc.", "topics": [ "get_sig_rec_similarity" ] }, { "page": "get_sig_similarity", "title": "Calculate Similarity between Identified Signatures and Reference Signatures", "topics": [ "get_sig_similarity" ] }, { "page": "get_tidy_association", "title": "Get Tidy Signature Association Results", "topics": [ "get_tidy_association" ] }, { "page": "group_enrichment", "title": "General Group Enrichment Analysis", "topics": [ "group_enrichment" ] }, { "page": "group_enrichment2", "title": "Group Enrichment Analysis with Subsets", "topics": [ "group_enrichment2" ] }, { "page": "handle_hyper_mutation", "title": "Handle Hypermutant Samples", "topics": [ "handle_hyper_mutation" ] }, { "page": "hello", "title": "Say Hello to Users", "topics": [ "hello" ] }, { "page": "MAF-class", "title": "Class MAF", "topics": [ "MAF", "MAF-class" ] }, { "page": "output_bootstrap", "title": "Output Signature Bootstrap Fitting Results", "topics": [ "output_bootstrap" ] }, { "page": "output_fit", "title": "Output Signature Fitting Results", "topics": [ "output_fit" ] }, { "page": "output_sig", "title": "Output Signature Results", "topics": [ "output_sig" ] }, { "page": "output_tally", "title": "Output Tally Result in Barplots", "topics": [ "output_tally" ] }, { "page": "read_copynumber", "title": "Read Absolute Copy Number Profile", "topics": [ "read_copynumber" ] }, { "page": "read_copynumber_ascat", "title": "Read Copy Number Data from ASCAT Result Files", "topics": [ "read_copynumber_ascat" ] }, { "page": "read_copynumber_seqz", "title": "Read Absolute Copy Number Profile from Sequenza Result Directory", "topics": [ "read_copynumber_seqz" ] }, { "page": "read_maf", "title": "Read MAF Files", "topics": [ "read_maf", "read_maf_minimal" ] }, { "page": "read_sv_as_rs", "title": "Read Structural Variation Data as RS object", "topics": [ "read_sv_as_rs" ] }, { "page": "read_vcf", "title": "Read VCF Files as MAF Object", "topics": [ "read_vcf" ] }, { "page": "read_xena_variants", "title": "Read UCSC Xena Variant Format Data as MAF Object", "topics": [ "read_xena_variants" ] }, { "page": "report_bootstrap_p_value", "title": "Report P Values from bootstrap Results", "topics": [ "report_bootstrap_p_value" ] }, { "page": "same_size_clustering", "title": "Same Size Clustering", "topics": [ "same_size_clustering" ] }, { "page": "scoring", "title": "Score Copy Number Profile", "topics": [ "scoring" ] }, { "page": "show_catalogue", "title": "Show Alteration Catalogue Profile", "topics": [ "show_catalogue" ] }, { "page": "show_cn_circos", "title": "Show Copy Number Profile in Circos", "topics": [ "show_cn_circos" ] }, { "page": "show_cn_components", "title": "Show Copy Number Components", "topics": [ "show_cn_components" ] }, { "page": "show_cn_distribution", "title": "Show Copy Number Distribution either by Length or Chromosome", "topics": [ "show_cn_distribution" ] }, { "page": "show_cn_features", "title": "Show Copy Number Feature Distributions", "topics": [ "show_cn_features" ] }, { "page": "show_cn_freq_circos", "title": "Show Copy Number Variation Frequency Profile with Circos", "topics": [ "show_cn_freq_circos" ] }, { "page": "show_cn_group_profile", "title": "Show Summary Copy Number Profile for Sample Groups", "topics": [ "show_cn_group_profile" ] }, { "page": "show_cn_profile", "title": "Show Sample Copy Number Profile", "topics": [ "show_cn_profile" ] }, { "page": "show_cor", "title": "A Simple and General Way for Association Analysis", "topics": [ "show_cor" ] }, { "page": "show_cosmic", "title": "Show Signature Information in Web Browser", "topics": [ "show_cosmic" ] }, { "page": "show_cosmic_sig_profile", "title": "Plot Reference (Mainly COSMIC) Signature Profile", "topics": [ "show_cosmic_sig_profile" ] }, { "page": "show_group_comparison", "title": "Plot Group Comparison Result", "topics": [ "show_group_comparison" ] }, { "page": "show_group_distribution", "title": "Show Groupped Variable Distribution", "topics": [ "show_group_distribution" ] }, { "page": "show_group_enrichment", "title": "Show Group Enrichment Result", "topics": [ "show_group_enrichment" ] }, { "page": "show_group_mapping", "title": "Map Groups using Sankey", "topics": [ "show_group_mapping" ] }, { "page": "show_groups", "title": "Show Signature Contribution in Clusters", "topics": [ "show_groups" ] }, { "page": "show_sig_bootstrap", "title": "Show Signature Bootstrap Analysis Results", "topics": [ "show_sig_bootstrap", "show_sig_bootstrap_error", "show_sig_bootstrap_exposure", "show_sig_bootstrap_stability" ] }, { "page": "show_sig_consensusmap", "title": "Show Signature Consensus Map", "topics": [ "show_sig_consensusmap" ] }, { "page": "show_sig_exposure", "title": "Plot Signature Exposure", "topics": [ "show_sig_exposure" ] }, { "page": "show_sig_feature_corrplot", "title": "Draw Corrplot for Signature Exposures and Other Features", "topics": [ "show_sig_feature_corrplot" ] }, { "page": "show_sig_fit", "title": "Show Signature Fit Result", "topics": [ "show_sig_fit" ] }, { "page": "show_sig_profile", "title": "Show Signature Profile", "topics": [ "show_sig_profile" ] }, { "page": "show_sig_profile_heatmap", "title": "Show Signature Profile with Heatmap", "topics": [ "show_sig_profile_heatmap" ] }, { "page": "show_sig_profile_loop", "title": "Show Signature Profile with Loop Way", "topics": [ "show_sig_profile_loop" ] }, { "page": "sig_auto_extract", "title": "Extract Signatures through the Automatic Relevance Determination 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"sig_modify_names", "sig_names", "sig_number", "sig_operation", "sig_signature" ] }, { "page": "sig_tally", "title": "Tally a Genomic Alteration Object", "topics": [ "sig_tally", "sig_tally.CopyNumber", "sig_tally.MAF", "sig_tally.RS" ] }, { "page": "sig_unify_extract", "title": "An Unified Interface to Extract Signatures", "topics": [ "sig_unify_extract" ] }, { "page": "sigprofiler", "title": "Extract Signatures with SigProfiler", "topics": [ "sigprofiler", "sigprofiler_extract", "sigprofiler_import", "sigprofiler_reorder" ] }, { "page": "simulated_catalogs", "title": "A List of Simulated SBS-96 Catalog Matrix", "topics": [ "simulated_catalogs" ] }, { "page": "simulation", "title": "Simulation Analysis", "topics": [ "simulate_catalogue", "simulate_catalogue_matrix", "simulate_signature", "simulation" ] }, { "page": "subset.CopyNumber", "title": "Subsetting CopyNumber object", "topics": [ "subset.CopyNumber" ] }, { "page": "transcript.hg19", "title": "Merged Transcript Location at 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