Package: sigminer 2.3.1

sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <doi:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <doi:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <doi:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.

Authors:Shixiang Wang [aut, cre], Ziyu Tao [aut], Huimin Li [aut], Tao Wu [aut], Xue-Song Liu [aut, ctb], Anand Mayakonda [ctb]

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sigminer.pdf |sigminer.html
sigminer/json (API)
NEWS

# Install sigminer in R:
install.packages('sigminer', repos = c('https://shixiangwang.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/shixiangwang/sigminer/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualization

115 exports 136 stars 4.91 score 105 dependencies 2 dependents 1.4k downloads

Last updated 14 days agofrom:01d1e938a07ed68d113054629d2608f3d36a1360

Exports::=.data.env%>%add_h_arrowadd_labelsas_labelas_namebp_attribute_activitybp_cluster_iter_listbp_extract_signaturesbp_extract_signatures_iterbp_get_clustered_sigsbp_get_rank_scorebp_get_sig_objbp_get_statsbp_show_surveybp_show_survey2CopyNumbercosineenquoenquosenrich_component_strand_biasexprget_adj_pget_Aneuploidy_scoreget_bayesian_resultget_cn_freq_tableget_cn_ploidyget_genome_annotationget_group_comparisonget_groupsget_intersect_sizeget_pLOH_scoreget_shannon_diversity_indexget_sig_cancer_type_indexget_sig_dbget_sig_exposureget_sig_feature_associationget_sig_rec_similarityget_sig_similarityget_tidy_associationgroup_enrichmentgroup_enrichment2handle_hyper_mutationhelloMAFoutput_bootstrapoutput_fitoutput_sigoutput_tallyread_copynumberread_copynumber_ascatread_copynumber_seqzread_mafread_maf_minimalread_sv_as_rsread_vcfread_xena_variantsreport_bootstrap_p_valuesame_size_clusteringscoringshow_catalogueshow_cn_circosshow_cn_componentsshow_cn_distributionshow_cn_featuresshow_cn_freq_circosshow_cn_group_profileshow_cn_profileshow_corshow_cosmicshow_cosmic_sig_profileshow_group_comparisonshow_group_distributionshow_group_enrichmentshow_group_mappingshow_groupsshow_sig_bootstrap_errorshow_sig_bootstrap_exposureshow_sig_bootstrap_stabilityshow_sig_consensusmapshow_sig_exposureshow_sig_feature_corrplotshow_sig_fitshow_sig_number_surveyshow_sig_number_survey2show_sig_profileshow_sig_profile_heatmapshow_sig_profile_loopsig_attrssig_auto_extractsig_convertsig_estimatesig_exposuresig_extractsig_fitsig_fit_bootstrapsig_fit_bootstrap_batchsig_modify_namessig_namessig_numbersig_signaturesig_tallysig_unify_extractsigprofiler_extractsigprofiler_importsigprofiler_reordersimulate_cataloguesimulate_catalogue_matrixsimulate_signaturesymsymstransform_seg_tableuse_color_style

Dependencies:abindbackportsBiobaseBiocGenericsBiocManagerbootbriobroomcallrcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11crayondata.tabledescdiffobjdigestDNAcopydoParalleldplyrevaluatefansifarverforeachfsfurrrfuturegenericsggplot2ggpubrggrepelggsciggsignifglobalsgluegridBasegridExtragtableisobanditeratorsjsonlitelabelinglatticelifecyclelistenvlme4maftoolsmagrittrMASSMatrixMatrixModelsmgcvminqamunsellnlmenloptrNMFnnetnumDerivparallellypbkrtestpillarpkgbuildpkgconfigpkgloadplyrpolynompraiseprocessxpspurrrquantregR6RColorBrewerRcppRcppEigenregistryrematch2reshape2RhtslibrlangrngtoolsrprojrootrstatixscalesSparseMstringistringrsurvivaltestthattibbletidyrtidyselectutf8vctrsviridisLitewaldowithrzlibbioc

A Quick Start of sigminer Package

Rendered fromsigminer.Rmdusingknitr::rmarkdownon Jun 07 2024.

Last update: 2024-03-01
Started: 2019-04-20

Analyze Copy Number Signatures with sigminer

Rendered fromcnsignature.Rmdusingknitr::rmarkdownon Jun 07 2024.

Last update: 2023-03-15
Started: 2022-06-30

Readme and manuals

Help Manual

Help pageTopics
Add Horizontal Arrow with Text Label to a ggplotadd_h_arrow
Add Text Labels to a ggplotadd_labels
A Best Practice for Signature Extraction and Exposure (Activity) Attributionbp bp_attribute_activity bp_cluster_iter_list bp_extract_signatures bp_extract_signatures_iter bp_get_clustered_sigs bp_get_rank_score bp_get_sig_obj bp_get_stats bp_show_survey bp_show_survey2
Location of Centromeres at Genome Build hg19centromeres.hg19
Location of Centromeres at Genome Build hg38centromeres.hg38
Location of Centromeres at Genome Build mm10centromeres.mm10
Location of Centromeres at Genome Build mm9centromeres.mm9
Location of Centromeres at Genome Build T2Tcentromeres.T2T
Chromosome Size of Genome Build hg19chromsize.hg19
Chromosome Size of Genome Build hg38chromsize.hg38
Chromosome Size of Genome Build mm10chromsize.mm10
Chromosome Size of Genome Build mm9chromsize.mm9
Chromosome Size of Genome Build T2Tchromsize.T2T
Classification Table of Copy Number Features Devised by Wang et al. for Method 'W'CN.features
Class CopyNumberCopyNumber CopyNumber-class
Calculate Cosine Measurescosine
Location of Chromosome Cytobands at Genome Build hg19cytobands.hg19
Location of Chromosome Cytobands at Genome Build hg38cytobands.hg38
Location of Chromosome Cytobands at Genome Build mm10cytobands.mm10
Location of Chromosome Cytobands at Genome Build mm9cytobands.mm9
Location of Chromosome Cytobands at Genome Build T2Tcytobands.T2T
Performs Strand Bias Enrichment Analysis for a Given Sample-by-Component Matrixenrich_component_strand_bias
Get Adjust P Values from Group Comparisonget_adj_p
Get Aneuploidy Score from Copy Number Profileget_Aneuploidy_score
Get Specified Bayesian NMF Result from Runget_bayesian_result
Get CNV Frequency Tableget_cn_freq_table
Get Ploidy from Absolute Copy Number Profileget_cn_ploidy
Get Genome Annotationget_genome_annotation
Get Comparison Result between Signature Groupsget_group_comparison
Get Sample Groups from Signature Decomposition Informationget_groups
Get Overlap Size between Interval x and yget_intersect_size
Get proportions of pLOH score from Allele Specific Copy Number Profileget_pLOH_score
Get Shannon Diversity Index for Signaturesget_shannon_diversity_index
Obtain Signature Index for Cancer Typesget_sig_cancer_type_index
Get Curated Reference Signature Databaseget_sig_db
Get Signature Exposure from 'Signature' Objectget_sig_exposure
Calculate Association between Signature Exposures and Other Featuresget_sig_feature_association
Get Reconstructed Profile Cosine Similarity, RSS, etc.get_sig_rec_similarity
Calculate Similarity between Identified Signatures and Reference Signaturesget_sig_similarity
Get Tidy Signature Association Resultsget_tidy_association
General Group Enrichment Analysisgroup_enrichment
Group Enrichment Analysis with Subsetsgroup_enrichment2
Handle Hypermutant Sampleshandle_hyper_mutation
Say Hello to Usershello
Class MAFMAF MAF-class
Output Signature Bootstrap Fitting Resultsoutput_bootstrap
Output Signature Fitting Resultsoutput_fit
Output Signature Resultsoutput_sig
Output Tally Result in Barplotsoutput_tally
Read Absolute Copy Number Profileread_copynumber
Read Copy Number Data from ASCAT Result Filesread_copynumber_ascat
Read Absolute Copy Number Profile from Sequenza Result Directoryread_copynumber_seqz
Read MAF Filesread_maf read_maf_minimal
Read Structural Variation Data as RS objectread_sv_as_rs
Read VCF Files as MAF Objectread_vcf
Read UCSC Xena Variant Format Data as MAF Objectread_xena_variants
Report P Values from bootstrap Resultsreport_bootstrap_p_value
Same Size Clusteringsame_size_clustering
Score Copy Number Profilescoring
Show Alteration Catalogue Profileshow_catalogue
Show Copy Number Profile in Circosshow_cn_circos
Show Copy Number Componentsshow_cn_components
Show Copy Number Distribution either by Length or Chromosomeshow_cn_distribution
Show Copy Number Feature Distributionsshow_cn_features
Show Copy Number Variation Frequency Profile with Circosshow_cn_freq_circos
Show Summary Copy Number Profile for Sample Groupsshow_cn_group_profile
Show Sample Copy Number Profileshow_cn_profile
A Simple and General Way for Association Analysisshow_cor
Show Signature Information in Web Browsershow_cosmic
Plot Reference (Mainly COSMIC) Signature Profileshow_cosmic_sig_profile
Plot Group Comparison Resultshow_group_comparison
Show Groupped Variable Distributionshow_group_distribution
Show Group Enrichment Resultshow_group_enrichment
Map Groups using Sankeyshow_group_mapping
Show Signature Contribution in Clustersshow_groups
Show Signature Bootstrap Analysis Resultsshow_sig_bootstrap show_sig_bootstrap_error show_sig_bootstrap_exposure show_sig_bootstrap_stability
Show Signature Consensus Mapshow_sig_consensusmap
Plot Signature Exposureshow_sig_exposure
Draw Corrplot for Signature Exposures and Other Featuresshow_sig_feature_corrplot
Show Signature Fit Resultshow_sig_fit
Show Signature Profileshow_sig_profile
Show Signature Profile with Heatmapshow_sig_profile_heatmap
Show Signature Profile with Loop Wayshow_sig_profile_loop
Extract Signatures through the Automatic Relevance Determination Techniquesig_auto_extract
Convert Signatures between different Genomic Distribution of Componentssig_convert
Estimate Signature Numbershow_sig_number_survey show_sig_number_survey2 sig_estimate
Extract Signatures through NMFsig_extract
Fit Signature Exposures with Linear Combination Decompositionsig_fit
Obtain Bootstrap Distribution of Signature Exposures of a Certain Tumor Samplesig_fit_bootstrap
Exposure Instability Analysis of Signature Exposures with Bootstrappingsig_fit_bootstrap_batch
Obtain or Modify Signature Informationsig_attrs sig_exposure sig_modify_names sig_names sig_number sig_operation sig_signature
Tally a Genomic Alteration Objectsig_tally sig_tally.CopyNumber sig_tally.MAF sig_tally.RS
An Unified Interface to Extract Signaturessig_unify_extract
Extract Signatures with SigProfilersigprofiler sigprofiler_extract sigprofiler_import sigprofiler_reorder
A List of Simulated SBS-96 Catalog Matrixsimulated_catalogs
Simulation Analysissimulate_catalogue simulate_catalogue_matrix simulate_signature simulation
Subsetting CopyNumber objectsubset.CopyNumber
Merged Transcript Location at Genome Build hg19transcript.hg19
Merged Transcript Location at Genome Build hg38transcript.hg38
Merged Transcript Location at Genome Build mm10transcript.mm10
Merged Transcript Location at Genome Build mm9transcript.mm9
Merged Transcript Location at Genome Build T2Ttranscript.T2T
Transform Copy Number Tabletransform_seg_table
Set Color Style for Plottinguse_color_style