Files in ShixiangWang/sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/pkgdown.yaml

.gitignore

.gitmodules

CRAN-SUBMISSION

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/CN-mutex-classification-method.R R/RcppExports.R R/add_h_arrow.R R/add_labels.R R/assert.R R/bayesianNMF.R R/best_practice.R R/best_practice_helper.R R/class.R R/cosine.R R/data.R R/enrich_component_strand_bias.R R/find_enriched_signature.R R/generate_matrices.R R/get.R R/get_Aneuploidy_score.R R/get_adj_p.R R/get_bayesian_result.R R/get_cn_freq_table.R R/get_cn_ploidy.R R/get_genome_annotation.R R/get_group_comparison.R R/get_groups.R R/get_intersect_size.R R/get_pLOH_score.R R/get_reconstructed_similarity.R R/get_shannon_diversity_index.R R/get_sig_cancer_type_index.R R/get_sig_db.R R/get_sig_exposure.R R/get_sig_feature_association.R R/get_sig_optimal_exposure.R R/get_sig_similarity.R R/get_sv.R R/get_tidy_association.R R/globalVariables.R R/group_enrichment.R R/handle_hyper_mutation.R R/hello.R R/helper_create_chunks.R R/helper_create_colormap.R R/helper_derive_cn_features.R R/helper_join_segments.R R/helper_normalize_by_feature.R R/helper_scale_nmf_matrix.R R/helper_sort_signature.R R/output.R R/read_copynumber.R R/read_copynumber_ascat.R R/read_copynumber_seqz.R R/read_maf.R R/read_vcf.R R/same_size_clustering.R R/scoring.R R/show_catalogue.R R/show_cn_circos.R R/show_cn_components.R R/show_cn_distribution.R R/show_cn_features.R R/show_cn_freq_circos.R R/show_cn_group_profile.R R/show_cn_profile.R R/show_cor.R R/show_cosmic_signature.R R/show_cosmic_signature_profile.R R/show_group_comparison.R R/show_group_distribution.R R/show_group_enrichment.R R/show_group_mapping.R R/show_groups.R R/show_sig_bootstrap.R R/show_sig_consensusmap.R R/show_sig_exposure.R R/show_sig_feature_corrplot.R R/show_sig_fit.R R/show_sig_profile.R R/show_sig_profile_heatmap.R R/show_sig_profile_loop.R R/sig_auto_extract.R R/sig_convert.R R/sig_estimate.R R/sig_extract.R R/sig_fit.R R/sig_fit_bootstrap.R R/sig_fit_bootstrap_batch.R R/sig_tally.R R/sig_unify_extract.R R/sigflow.R R/sigminer.R R/signature_obj_operation.R R/sigprofiler.R R/simulation.R R/transform_seg_table.R R/utils-pipe.R R/utils-tidy-eval.R R/utils.R R/utils_mem.R R/zzz.R README.Rmd README.md

_pkgdown.yml

codecov.yml

cran_check.R

data-raw/BRCA-RS.xlsx

data-raw/CN-features.R

data-raw/COSMIC_Mutational_Signatures_v3.1.xlsx

data-raw/Cohort-CNS.R data-raw/Cohort-RS.R

data-raw/DBS_signatures_genome_builds.xlsx

data-raw/NC-Ref-Sigs.xlsx

data-raw/NC-Supp-data.xlsx

data-raw/Nature-Cancer-Sigs.R

data-raw/PCAWG.CNS.xlsx

data-raw/SBS_signatures_genome_builds.xlsx

data-raw/T2T.R

data-raw/TCGA.CNS.xlsx

data-raw/USARC-Metadata-and-SV.xlsx

data-raw/USARC.CNS.xlsx

data-raw/USARC.RS.xlsx

data-raw/ce11_genome.R

data-raw/chm13.draft_v2.0.cen_mask.bed

data-raw/chm13v2.0_censat_v2.0.bed

data-raw/chm13v2.0_cytobands_allchrs.bed

data-raw/cytobands.R

data-raw/mm10.chrom.sizes.txt

data-raw/mm10.cytoBand.txt.gz

data-raw/mm10.gap.txt.gz

data-raw/mm9.chrom.sizes

data-raw/mm9.cytoBand.txt.gz

data-raw/mm9.gap

data-raw/mouse_genome.R data-raw/ref_signatures.R data-raw/simulated_catalogs.R

data-raw/sv.RData

data-raw/transcript_region.R

data-raw/ucsc.hg19.cytoband.RData

data-raw/ucsc.hg38.cytoband.RData

data/CN.features.rda

data/centromeres.T2T.rda

data/centromeres.hg19.rda

data/centromeres.hg38.rda

data/centromeres.mm10.rda

data/centromeres.mm9.rda

data/chromsize.T2T.rda

data/chromsize.hg19.rda

data/chromsize.hg38.rda

data/chromsize.mm10.rda

data/chromsize.mm9.rda

data/cytobands.T2T.rda

data/cytobands.hg19.rda

data/cytobands.hg38.rda

data/cytobands.mm10.rda

data/cytobands.mm9.rda

data/simulated_catalogs.rda

data/transcript.T2T.rda

data/transcript.hg19.rda

data/transcript.hg38.rda

data/transcript.mm10.rda

data/transcript.mm9.rda

inst/CITATION

inst/extdata/CN40-Map.txt

inst/extdata/CN48-Map.txt

inst/extdata/CNS_signatures_PCAWG176.rds

inst/extdata/CNS_signatures_TCGA.rds

inst/extdata/CNS_signatures_TCGA176.rds

inst/extdata/CNS_signatures_USARC.rds

inst/extdata/DBS_signatures.rds

inst/extdata/DBS_signatures_list.rds

inst/extdata/ID_signatures.rds

inst/extdata/RS_signatures_BRCA560.rds

inst/extdata/RS_signatures_Nik_lab.rds

inst/extdata/RS_signatures_Nik_lab_Organ.rds

inst/extdata/RS_signatures_USARC.rds

inst/extdata/SBS_signatures.rds

inst/extdata/SBS_signatures_Nik_lab.rds

inst/extdata/SBS_signatures_Nik_lab_Organ.rds

inst/extdata/SBS_signatures_list.rds

inst/extdata/TSB_signatures.rds

inst/extdata/asso_data.RData

inst/extdata/cosmic2_record_by_cancer.rds

inst/extdata/e1.RData

inst/extdata/metastatic_tumor.segtab.txt

inst/extdata/signature_record_by_cancer.rds

inst/extdata/test1.vcf

inst/extdata/test2.vcf

inst/extdata/test3.vcf

inst/extdata/toy_cn.RData

inst/extdata/toy_cnlist.RData

inst/extdata/toy_copynumber.RData

inst/extdata/toy_copynumber_signature_by_W.RData

inst/extdata/toy_copynumber_tally_W.RData

inst/extdata/toy_mutational_signature.RData

inst/extdata/toy_segTab.RData

inst/extdata/toy_sv.rds

inst/figures/array2.png

inst/figures/sigminer.png

inst/py/nmf.py

inst/test/test.R inst/test/test_get_sv.R inst/test/use_hexsticker.R man/CN.features.Rd man/CopyNumber-class.Rd man/MAF-class.Rd man/add_h_arrow.Rd man/add_labels.Rd man/bp.Rd man/centromeres.T2T.Rd man/centromeres.hg19.Rd man/centromeres.hg38.Rd man/centromeres.mm10.Rd man/centromeres.mm9.Rd man/chromsize.T2T.Rd man/chromsize.hg19.Rd man/chromsize.hg38.Rd man/chromsize.mm10.Rd man/chromsize.mm9.Rd man/cosine.Rd man/cytobands.T2T.Rd man/cytobands.hg19.Rd man/cytobands.hg38.Rd man/cytobands.mm10.Rd man/cytobands.mm9.Rd man/enrich_component_strand_bias.Rd

man/figures/README-unnamed-chunk-1-1.png

man/figures/README-unnamed-chunk-2-1.png

man/figures/README-unnamed-chunk-3-1.png

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man/figures/README-unnamed-chunk-9-1.png

man/figures/logo.png

man/get_Aneuploidy_score.Rd man/get_adj_p.Rd man/get_bayesian_result.Rd man/get_cn_freq_table.Rd man/get_cn_ploidy.Rd man/get_genome_annotation.Rd man/get_group_comparison.Rd man/get_groups.Rd man/get_intersect_size.Rd man/get_pLOH_score.Rd man/get_shannon_diversity_index.Rd man/get_sig_cancer_type_index.Rd man/get_sig_db.Rd man/get_sig_exposure.Rd man/get_sig_feature_association.Rd man/get_sig_rec_similarity.Rd man/get_sig_similarity.Rd man/get_tidy_association.Rd man/group_enrichment.Rd man/group_enrichment2.Rd man/handle_hyper_mutation.Rd man/hello.Rd man/output_bootstrap.Rd man/output_fit.Rd man/output_sig.Rd man/output_tally.Rd man/pipe.Rd man/read_copynumber.Rd man/read_copynumber_ascat.Rd man/read_copynumber_seqz.Rd man/read_maf.Rd man/read_sv_as_rs.Rd man/read_vcf.Rd man/read_xena_variants.Rd man/report_bootstrap_p_value.Rd man/same_size_clustering.Rd man/scoring.Rd man/show_catalogue.Rd man/show_cn_circos.Rd man/show_cn_components.Rd man/show_cn_distribution.Rd man/show_cn_features.Rd man/show_cn_freq_circos.Rd man/show_cn_group_profile.Rd man/show_cn_profile.Rd man/show_cor.Rd man/show_cosmic.Rd man/show_cosmic_sig_profile.Rd man/show_group_comparison.Rd man/show_group_distribution.Rd man/show_group_enrichment.Rd man/show_group_mapping.Rd man/show_groups.Rd man/show_sig_bootstrap.Rd man/show_sig_consensusmap.Rd man/show_sig_exposure.Rd man/show_sig_feature_corrplot.Rd man/show_sig_fit.Rd man/show_sig_profile.Rd man/show_sig_profile_heatmap.Rd man/show_sig_profile_loop.Rd man/sig_auto_extract.Rd man/sig_convert.Rd man/sig_estimate.Rd man/sig_extract.Rd man/sig_fit.Rd man/sig_fit_bootstrap.Rd man/sig_fit_bootstrap_batch.Rd man/sig_operation.Rd man/sig_tally.Rd man/sig_unify_extract.Rd man/sigminer-package.Rd man/sigprofiler.Rd man/simulated_catalogs.Rd man/simulation.Rd man/subset.CopyNumber.Rd man/tidyeval.Rd man/transcript.T2T.Rd man/transcript.hg19.Rd man/transcript.hg38.Rd man/transcript.mm10.Rd man/transcript.mm9.Rd man/transform_seg_table.Rd man/use_color_style.Rd

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pkgdown/favicon/apple-touch-icon.png

pkgdown/favicon/favicon-16x16.png

pkgdown/favicon/favicon-32x32.png

pkgdown/favicon/favicon.ico

sigminer.Rproj

src/.gitignore

src/RcppExports.cpp

src/calc_cosine.cpp

src/get_intersect_size.cpp

vignettes/.gitignore

vignettes/cnsignature.Rmd

vignettes/e1.rds

vignettes/sigminer.Rmd

ShixiangWang/sigminer documentation built on March 16, 2024, 12:30 p.m.

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ShixiangWang/sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Files in ShixiangWang/sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

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ShixiangWang/sigminer Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Files in ShixiangWang/sigminer Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

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ShixiangWang/sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Files in ShixiangWang/sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations