Files in sigminer
Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
LICENSE
R/sig_unify_extract.R
R/RcppExports.R
R/globalVariables.R
R/bayesianNMF.R
R/show_cor.R
R/sigminer.R
R/get_pLOH_score.R
R/show_sig_consensusmap.R
R/get.R
R/get_reconstructed_similarity.R
R/get_sv.R
R/utils_mem.R
R/assert.R
R/get_sig_cancer_type_index.R
R/read_copynumber.R
R/group_enrichment.R
R/get_cn_freq_table.R
R/find_enriched_signature.R
R/show_catalogue.R
R/show_group_distribution.R
R/get_intersect_size.R
R/show_sig_profile_loop.R
R/output.R
R/generate_matrices.R
R/get_sig_exposure.R
R/utils-pipe.R
R/get_Aneuploidy_score.R
R/get_genome_annotation.R
R/read_maf.R
R/transform_seg_table.R
R/get_sig_db.R
R/helper_scale_nmf_matrix.R
R/show_sig_profile.R
R/sig_auto_extract.R
R/show_cn_group_profile.R
R/helper_create_colormap.R
R/sig_convert.R
R/sig_fit_bootstrap_batch.R
R/helper_create_chunks.R
R/get_adj_p.R
R/simulation.R
R/show_sig_bootstrap.R
R/handle_hyper_mutation.R
R/data.R
R/show_groups.R
R/show_sig_fit.R
R/hello.R
R/get_cn_ploidy.R
R/enrich_component_strand_bias.R
R/read_copynumber_seqz.R
R/helper_join_segments.R
R/sig_estimate.R
R/show_sig_feature_corrplot.R
R/sig_extract.R
R/best_practice_helper.R
R/sigflow.R
R/helper_normalize_by_feature.R
R/show_sig_exposure.R
R/show_cn_freq_circos.R
R/show_sig_profile_heatmap.R
R/get_sig_optimal_exposure.R
R/best_practice.R
R/get_bayesian_result.R
R/add_h_arrow.R
R/sigprofiler.R
R/show_cn_components.R
R/get_sig_feature_association.R
R/helper_derive_cn_features.R
R/show_cn_profile.R
R/show_group_enrichment.R
R/read_vcf.R
R/show_cosmic_signature_profile.R
R/get_sig_similarity.R
R/get_groups.R
R/get_tidy_association.R
R/zzz.R
R/add_labels.R
R/show_cn_circos.R
R/sig_tally.R
R/helper_sort_signature.R
R/get_group_comparison.R
R/cosine.R
R/CN-mutex-classification-method.R
R/get_shannon_diversity_index.R
R/utils-tidy-eval.R
R/show_cn_distribution.R
R/sig_fit_bootstrap.R
R/sig_fit.R
R/show_cosmic_signature.R
R/show_cn_features.R
R/class.R
R/show_group_mapping.R
R/show_group_comparison.R
R/read_copynumber_ascat.R
R/same_size_clustering.R
R/utils.R
R/scoring.R
R/signature_obj_operation.R
src/RcppExports.cpp
src/get_intersect_size.cpp
src/calc_cosine.cpp
inst/CITATION
inst/doc/sigminer.R
inst/doc/sigminer.html
inst/doc/sigminer.Rmd
inst/doc/cnsignature.Rmd
inst/doc/cnsignature.R
inst/doc/cnsignature.html
inst/py/nmf.py
inst/extdata/metastatic_tumor.segtab.txt
inst/extdata/toy_sv.rds
inst/extdata/toy_cn.RData
inst/extdata/toy_copynumber_signature_by_W.RData
inst/extdata/RS_signatures_Nik_lab_Organ.rds
inst/extdata/signature_record_by_cancer.rds
inst/extdata/toy_copynumber.RData
inst/extdata/toy_cnlist.RData
inst/extdata/CNS_signatures_USARC.rds
inst/extdata/RS_signatures_USARC.rds
inst/extdata/SBS_signatures_Nik_lab_Organ.rds
inst/extdata/test1.vcf
inst/extdata/DBS_signatures.rds
inst/extdata/SBS_signatures_Nik_lab.rds
inst/extdata/toy_segTab.RData
inst/extdata/SBS_signatures.rds
inst/extdata/toy_mutational_signature.RData
inst/extdata/CNS_signatures_TCGA176.rds
inst/extdata/TSB_signatures.rds
inst/extdata/CNS_signatures_PCAWG176.rds
inst/extdata/test2.vcf
inst/extdata/ce11_gene_info.rds
inst/extdata/ID_signatures.rds
inst/extdata/CNS_signatures_TCGA.rds
inst/extdata/CN40-Map.txt
inst/extdata/test3.vcf
inst/extdata/asso_data.RData
inst/extdata/CN48-Map.txt
inst/extdata/SBS_signatures_list.rds
inst/extdata/toy_copynumber_tally_W.RData
inst/extdata/RS_signatures_Nik_lab.rds
inst/extdata/DBS_signatures_list.rds
inst/extdata/RS_signatures_BRCA560.rds
inst/extdata/cosmic2_record_by_cancer.rds
inst/extdata/e1.RData
build/vignette.rds
build/partial.rdb
vignettes/sigminer.Rmd
vignettes/cnsignature.Rmd
vignettes/e1.rds
data/transcript.hg38.rda
data/transcript.mm10.rda
data/cytobands.mm9.rda
data/CN.features.rda
data/simulated_catalogs.rda
data/cytobands.mm10.rda
data/centromeres.hg38.rda
data/chromsize.mm10.rda
data/chromsize.mm9.rda
data/centromeres.mm9.rda
data/transcript.mm9.rda
data/centromeres.hg19.rda
data/cytobands.hg38.rda
data/cytobands.hg19.rda
data/chromsize.hg19.rda
data/centromeres.mm10.rda
data/transcript.hg19.rda
data/chromsize.hg38.rda
man/cosine.Rd
man/MAF-class.Rd
man/show_sig_profile_heatmap.Rd
man/sig_unify_extract.Rd
man/transcript.hg38.Rd
man/show_cn_group_profile.Rd
man/show_sig_profile_loop.Rd
man/get_sig_rec_similarity.Rd
man/transcript.hg19.Rd
man/show_sig_profile.Rd
man/get_sig_db.Rd
man/sigminer-package.Rd
man/read_copynumber_ascat.Rd
man/transform_seg_table.Rd
man/show_cn_circos.Rd
man/chromsize.mm9.Rd
man/output_fit.Rd
man/enrich_component_strand_bias.Rd
man/show_cn_freq_circos.Rd
man/show_cn_distribution.Rd
man/tidyeval.Rd
man/subset.CopyNumber.Rd
man/show_sig_bootstrap.Rd
man/get_pLOH_score.Rd
man/get_genome_annotation.Rd
man/sig_fit_bootstrap_batch.Rd
man/output_bootstrap.Rd
man/sigprofiler.Rd
man/sig_auto_extract.Rd
man/get_group_comparison.Rd
man/chromsize.hg38.Rd
man/show_cor.Rd
man/show_cosmic_sig_profile.Rd
man/show_cn_features.Rd
man/centromeres.hg38.Rd
man/show_catalogue.Rd
man/get_Aneuploidy_score.Rd
man/group_enrichment2.Rd
man/get_sig_cancer_type_index.Rd
man/show_groups.Rd
man/add_h_arrow.Rd
man/CopyNumber-class.Rd
man/output_tally.Rd
man/report_bootstrap_p_value.Rd
man/chromsize.mm10.Rd
man/show_group_mapping.Rd
man/cytobands.mm10.Rd
man/get_sig_similarity.Rd
man/show_sig_feature_corrplot.Rd
man/get_shannon_diversity_index.Rd
man/output_sig.Rd
man/cytobands.mm9.Rd
man/simulation.Rd
man/read_vcf.Rd
man/same_size_clustering.Rd
man/sig_extract.Rd
man/sig_fit_bootstrap.Rd
man/get_sig_exposure.Rd
man/bp.Rd
man/sig_fit.Rd
man/chromsize.hg19.Rd
man/read_copynumber_seqz.Rd
man/read_sv_as_rs.Rd
man/CN.features.Rd
man/simulated_catalogs.Rd
man/show_cosmic.Rd
man/show_sig_exposure.Rd
man/pipe.Rd
man/centromeres.hg19.Rd
man/centromeres.mm9.Rd
man/sig_estimate.Rd
man/centromeres.mm10.Rd
man/get_tidy_association.Rd
man/get_cn_ploidy.Rd
man/show_cn_profile.Rd
man/show_group_comparison.Rd
man/show_group_distribution.Rd
man/transcript.mm10.Rd
man/get_cn_freq_table.Rd
man/read_maf.Rd
man/read_copynumber.Rd
man/scoring.Rd
man/group_enrichment.Rd
man/hello.Rd
man/cytobands.hg38.Rd
man/transcript.mm9.Rd
man/get_sig_feature_association.Rd
man/show_sig_consensusmap.Rd
man/use_color_style.Rd
man/read_xena_variants.Rd
man/handle_hyper_mutation.Rd
man/show_group_enrichment.Rd
man/show_cn_components.Rd
man/sig_convert.Rd
man/sig_operation.Rd
man/get_intersect_size.Rd
man/show_sig_fit.Rd
man/get_adj_p.Rd
man/add_labels.Rd
man/sig_tally.Rd
man/get_groups.Rd
man/cytobands.hg19.Rd
man/get_bayesian_result.Rd
man/figures/README-unnamed-chunk-3-1.png
man/figures/README-unnamed-chunk-8-1.png
man/figures/logo.png
man/figures/README-unnamed-chunk-2-1.png
man/figures/README-unnamed-chunk-1-1.png
man/figures/README-unnamed-chunk-9-1.png
man/figures/README-unnamed-chunk-4-1.png
man/figures/README-unnamed-chunk-7-1.png
man/figures/README-unnamed-chunk-6-1.png
man/figures/README-unnamed-chunk-5-1.png
