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

MD5
NEWS.md README.md
NAMESPACE
DESCRIPTION
LICENSE
R/RcppExports.R R/globalVariables.R R/bayesianNMF.R R/show_cor.R R/sigminer.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/show_sig_profile_loop.R R/output.R R/generate_matrices.R R/get_sig_exposure.R R/utils-pipe.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/same_size_clustering.R R/utils.R R/scoring.R R/signature_obj_operation.R
src/RcppExports.cpp
src/calc_cosine.cpp
inst/CITATION
inst/doc/sigminer.R
inst/doc/sigminer.html
inst/doc/sigminer.Rmd
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_copynumber_signature_by_M.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/TSB_signatures.rds
inst/extdata/test2.vcf
inst/extdata/ID_signatures.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/toy_copynumber_tally_M.RData
inst/extdata/cosmic2_record_by_cancer.rds
inst/extdata/e1.RData
build/vignette.rds
build/partial.rdb
vignettes/sigminer.Rmd
vignettes/e1.rds
data/transcript.hg38.rda
data/transcript.mm10.rda
data/CN.features.rda
data/simulated_catalogs.rda
data/cytobands.mm10.rda
data/centromeres.hg38.rda
data/chromsize.mm10.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/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/transform_seg_table.Rd man/show_cn_circos.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_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/sigminer.Rd man/show_cosmic_sig_profile.Rd man/show_cn_features.Rd man/centromeres.hg38.Rd man/show_catalogue.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/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/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/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/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
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man/figures/logo.png
man/figures/README-unnamed-chunk-2-1.png
man/figures/README-unnamed-chunk-1-1.png
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sigminer documentation built on April 1, 2021, 5:06 p.m.