Files in caravagnalab/CNAqc
CNAqc - Copy Number Analysis quality check
.DS_Store
.Rbuildignore
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
DriverDBv3.rda
LICENSE
LICENSE.md
NAMESPACE
NEWS
R/.Rapp.history
R/CNAqc-package.R
R/advanced_phasing.R
R/analyze_peaks.R
R/annotate_variants.R
R/assign_sbs_contexts.R
R/auto_tolerance.R
R/blank_genome.R
R/compute_CCF.R
R/data.R
R/detect_arm_overfragmentation.R
R/detect_wg_overfragmentation.R
R/drivers.R
R/eplot.R
R/equations.R
R/evo_dynamics.R
R/fortify.R
R/general_peaks.R
R/get_prevalent_karyotype.R
R/get_reference.R
R/getters.R
R/init.R
R/inspect_segment.R
R/maf.R
R/maf_utils.R
R/map_mutations.R
R/mutation_multiplicity.R
R/parse_Battenberg.R
R/peak_algorithms.R
R/peak_detector.R
R/pipelines.R
R/plot_CCF.R
R/plot_arm_fragmentation.R
R/plot_cohort_CNA.R
R/plot_data_histogram.R
R/plot_genome_wide_mutations.R
R/plot_icon_cna.R
R/plot_karyotypes.R
R/plot_multisample_CNA.R
R/plot_multisample_driversA.R
R/plot_peaks_analysis.R
R/plot_qc.R
R/plot_segment_size_distribution.R
R/plot_segments.R
R/plot_smoothing.R
R/prepare_input_data.R
R/print.cnaqc.R
R/smooth_segments.R
R/subclonal_peaks.R
R/subsample.R
R/utils-pipe.R
R/utils_CCF.R
R/utils_fragmentation.R
R/utils_plot.R
R/vaf_functions.R
R/vep.R
R/zzz.R
README.Rmd
README.md
_config.yml
_pkgdown.yml
data/chr_coordinates_GRCh38.rda
data/chr_coordinates_hg19.rda
data/example_PCAWG.rda
data/example_dataset_CNAqc.rda
data/fpr_test.rda
data/gene_coordinates_GRCh38.rda
data/gene_coordinates_hg19.rda
data/intogen_drivers.rda
docs/404.html
docs/LICENSE-text.html
docs/LICENSE.html
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docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/CNAqc.html
docs/articles/a1_Introduction.html
docs/articles/a1_Introduction_files/figure-html/unnamed-chunk-12-1.png
docs/articles/a2_Plots.html
docs/articles/a2_Plots_files/figure-html/unnamed-chunk-10-1.png
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docs/articles/a9_automatic.html
docs/articles/index.html
docs/articles/logo_summary.png
docs/articles/peaks.png
docs/articles/sqz_pipe.png
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
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docs/favicon.ico
docs/index.html
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docs/logo.png
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CCF.html
docs/reference/CNA.html
docs/reference/CNA_gene.html
docs/reference/CNAqc-package.html
docs/reference/DriverDBv3.html
docs/reference/Mutations.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/SBS.html
docs/reference/SBS_counts.html
docs/reference/Sequenza_CNAqc.html
docs/reference/analyze_peaks.html
docs/reference/annotate_variants.html
docs/reference/as_maftools_cohort.html
docs/reference/as_maftools_obj.html
docs/reference/augment_with_maf.html
docs/reference/augment_with_vep.html
docs/reference/auto_tolerance-1.png
docs/reference/auto_tolerance-2.png
docs/reference/auto_tolerance.html
docs/reference/boostDM_drivers.html
docs/reference/chr_coordinates_GRCh38.html
docs/reference/chr_coordinates_hg19.html
docs/reference/compute_CCF-1.png
docs/reference/compute_CCF.html
docs/reference/detect_arm_overfragmentation.html
docs/reference/example_PCAWG.html
docs/reference/example_dataset_CNAqc.html
docs/reference/figures/logo.png
docs/reference/fpr_test.html
docs/reference/gene_coordinates_GRCh38.html
docs/reference/gene_coordinates_hg19.html
docs/reference/get_PASS_percentage.html
docs/reference/get_drivers.html
docs/reference/index.html
docs/reference/init.html
docs/reference/inspect_segment-1.png
docs/reference/inspect_segment-2.png
docs/reference/inspect_segment.html
docs/reference/intogen_drivers.html
docs/reference/parse_Battenberg.html
docs/reference/pipe.html
docs/reference/plot.cnaqc.html
docs/reference/plot_CCF-1.png
docs/reference/plot_CCF.html
docs/reference/plot_SBS.html
docs/reference/plot_arm_fragmentation-1.png
docs/reference/plot_arm_fragmentation.html
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docs/reference/plot_multisample_CNA.html
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docs/reference/plot_peaks_analysis.html
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docs/reference/plot_segments-1.png
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docs/reference/plot_smoothing.html
docs/reference/print.cnaqc.html
docs/reference/smooth_segments-1.png
docs/reference/smooth_segments.html
docs/reference/split_by_chromosome.html
docs/reference/subsample.html
docs/reference/subset_by_minimum_CCF-1.png
docs/reference/subset_by_minimum_CCF-2.png
docs/reference/subset_by_minimum_CCF.html
docs/reference/subset_by_segment_karyotype.html
docs/reference/subset_by_segment_minmutations.html
docs/reference/subset_by_segment_totalcn.html
docs/reference/subset_snvs.html
docs/reference/wt_mutant_alleles.html
docs/sitemap.xml
logo.png
man/CCF.Rd
man/CNA.Rd
man/CNA_gene.Rd
man/CNAqc-package.Rd
man/Mutations.Rd
man/SBS.Rd
man/SBS_counts.Rd
man/Sequenza_CNAqc.Rd
man/analyze_peaks.Rd
man/annotate_variants.Rd
man/as_maftools_cohort.Rd
man/as_maftools_obj.Rd
man/augment_with_maf.Rd
man/augment_with_vep.Rd
man/auto_tolerance.Rd
man/chr_coordinates_GRCh38.Rd
man/chr_coordinates_hg19.Rd
man/compute_CCF.Rd
man/detect_arm_overfragmentation.Rd
man/example_PCAWG.Rd
man/example_dataset_CNAqc.Rd
man/fpr_test.Rd
man/gene_coordinates_GRCh38.Rd
man/gene_coordinates_hg19.Rd
man/get_PASS_percentage.Rd
man/get_drivers.Rd
man/init.Rd
man/inspect_segment.Rd
man/intogen_drivers.Rd
man/parse_Battenberg.Rd
man/pipe.Rd
man/plot.cnaqc.Rd
man/plot_CCF.Rd
man/plot_SBS.Rd
man/plot_arm_fragmentation.Rd
man/plot_data_histogram.Rd
man/plot_gw_ccf.Rd
man/plot_gw_counts.Rd
man/plot_gw_depth.Rd
man/plot_gw_vaf.Rd
man/plot_icon_CNA.Rd
man/plot_karyotypes.Rd
man/plot_multisample_CNA.Rd
man/plot_peaks_analysis.Rd
man/plot_qc.Rd
man/plot_segment_size_distribution.Rd
man/plot_segments.Rd
man/plot_smoothing.Rd
man/print.cnaqc.Rd
man/smooth_segments.Rd
man/split_by_chromosome.Rd
man/subsample.Rd
man/subset_by_minimum_CCF.Rd
man/subset_by_segment_karyotype.Rd
man/subset_by_segment_minmutations.Rd
man/subset_by_segment_totalcn.Rd
man/subset_snvs.Rd
man/wt_mutant_alleles.Rd
nobuild/Exome_genes.zip
nobuild/annotate_drivers.R
nobuild/annotate_genes_from_locations.R
nobuild/boostDM_drivers.rda
nobuild/create_drivers_list.R
nobuild/data.R
nobuild/ensemble_exomes.R
nobuild/exones_GRCh38.rda
nobuild/exones_hg19.rda
nobuild/fix_peak_analysis.R
nobuild/intogen_ttypes.rda
nobuild/mutation_download_tab.txt
nobuild/package_template.R
nobuild/plot_cohort_CNA.R
nobuild/sampler.R
pkgdown/favicon/apple-touch-icon-120x120.png
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pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
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vignettes/.gitignore
vignettes/CNAqc.Rmd
vignettes/a1_Introduction.Rmd
vignettes/a2_Plots.Rmd
vignettes/a3_peaks_detection.Rmd
vignettes/a4_ccf_computation.Rmd
vignettes/a5_smoothing.Rmd
vignettes/a6_fragmentation.Rmd
vignettes/a7_example_MSeq.Rmd
vignettes/a8_annotate_variants.Rmd
vignettes/a9_automatic.Rmd
vignettes/logo_summary.png
vignettes/peaks.png
vignettes/sqz_pipe.png
