Package: sigminer 2.3.2
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:
sigminer_2.3.2.tar.gz
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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')) |
Bug tracker:https://github.com/shixiangwang/sigminer/issues
Pkgdown:https://shixiangwang.github.io
- CN.features - Classification Table of Copy Number Features Devised by Wang et al. for Method 'W'
- centromeres.T2T - Location of Centromeres at Genome Build T2T
- centromeres.hg19 - Location of Centromeres at Genome Build hg19
- centromeres.hg38 - Location of Centromeres at Genome Build hg38
- centromeres.mm10 - Location of Centromeres at Genome Build mm10
- centromeres.mm9 - Location of Centromeres at Genome Build mm9
- chromsize.T2T - Chromosome Size of Genome Build T2T
- chromsize.hg19 - Chromosome Size of Genome Build hg19
- chromsize.hg38 - Chromosome Size of Genome Build hg38
- chromsize.mm10 - Chromosome Size of Genome Build mm10
- chromsize.mm9 - Chromosome Size of Genome Build mm9
- cytobands.T2T - Location of Chromosome Cytobands at Genome Build T2T
- cytobands.hg19 - Location of Chromosome Cytobands at Genome Build hg19
- cytobands.hg38 - Location of Chromosome Cytobands at Genome Build hg38
- cytobands.mm10 - Location of Chromosome Cytobands at Genome Build mm10
- cytobands.mm9 - Location of Chromosome Cytobands at Genome Build mm9
- simulated_catalogs - A List of Simulated SBS-96 Catalog Matrix
- transcript.T2T - Merged Transcript Location at Genome Build T2T
- transcript.hg19 - Merged Transcript Location at Genome Build hg19
- transcript.hg38 - Merged Transcript Location at Genome Build hg38
- transcript.mm10 - Merged Transcript Location at Genome Build mm10
- transcript.mm9 - Merged Transcript Location at Genome Build mm9
bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualizationcpp
Last updated 2 months agofrom:2324df8584. Checks:OK: 8 NOTE: 1. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Dec 11 2024 |
R-4.5-win-x86_64 | OK | Dec 11 2024 |
R-4.5-linux-x86_64 | OK | Dec 11 2024 |
R-4.4-win-x86_64 | OK | Dec 11 2024 |
R-4.4-mac-x86_64 | OK | Dec 11 2024 |
R-4.4-mac-aarch64 | OK | Dec 11 2024 |
R-4.3-win-x86_64 | OK | Dec 11 2024 |
R-4.3-mac-x86_64 | OK | Dec 11 2024 |
R-4.3-mac-aarch64 | NOTE | Dec 11 2024 |
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:abindbackportsBiobaseBiocGenericsBiocManagerbootbroomcarcarDatacliclustercodetoolscolorspacecorrplotcowplotcpp11data.tableDerivdigestDNAcopydoBydoParalleldplyrfansifarverforeachFormulafurrrfuturegenericsggplot2ggpubrggrepelggsciggsignifglobalsgluegridBasegridExtragtableisobanditeratorslabelinglatticelifecyclelistenvlme4maftoolsmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellnlmenloptrNMFnnetnumDerivparallellypbkrtestpheatmappillarpkgconfigplyrpolynompurrrquantregR6RColorBrewerRcppRcppEigenregistryreshape2RhtslibrlangrngtoolsrstatixscalesSparseMstringistringrsurvivaltibbletidyrtidyselectutf8vctrsviridisLitewithrzlibbioc