Files in whtns/numbat
Haplotype-Aware CNV Analysis from scRNA-Seq
.Rbuildignore
.circleci/config.yml
.gitattributes
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/RcppExports.R
R/class.R
R/data.R
R/genotyping.R
R/hmm.R
R/main.R
R/poilog.R
R/trees.R
R/utils.R
R/vis.R
R/zzz.R
README.md
_pkgdown.yml
data-raw/prep_data.R
data/acen_hg19.rda
data/acen_hg38.rda
data/annot_ref.rda
data/bulk_example.rda
data/chrom_sizes_hg19.rda
data/chrom_sizes_hg38.rda
data/count_mat_example.rda
data/count_mat_ref.rda
data/df_allele_example.rda
data/gaps_hg19.rda
data/gaps_hg38.rda
data/gexp_roll_example.rda
data/gtf_hg19.rda
data/gtf_hg38.rda
data/hc_example.rda
data/joint_post_example.rda
data/mut_graph_example.rda
data/phylogeny_example.rda
data/pre_likelihood_hmm.rda
data/ref_hca.rda
data/ref_hca_counts.rda
data/segs_example.rda
data/vcf_meta.rda
docker/Dockerfile.rbase
docker/Dockerfile.rstudio
docs/404.html
docs/apple-touch-icon-120x120.png
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/hmm.html
docs/articles/hmm_files/figure-html/unnamed-chunk-4-1.png
docs/articles/hmm_files/figure-html/unnamed-chunk-5-1.png
docs/articles/hmm_files/figure-html/unnamed-chunk-6-1.png
docs/articles/hmm_files/figure-html/unnamed-chunk-8-1.png
docs/articles/index.html
docs/articles/numbat.html
docs/articles/results.html
docs/articles/results_files/figure-html/unnamed-chunk-11-1.png
docs/articles/results_files/figure-html/unnamed-chunk-12-1.png
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docs/authors.html
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docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
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docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Modes.html
docs/reference/Numbat.html
docs/reference/aggregate_counts.html
docs/reference/analyze_bulk.html
docs/reference/annot_cm.html
docs/reference/annot_consensus.html
docs/reference/annot_haplo_segs.html
docs/reference/annot_segs.html
docs/reference/annot_superclones.html
docs/reference/annot_theta_roll.html
docs/reference/approx_phi_post.html
docs/reference/approx_theta_post.html
docs/reference/binary_entropy.html
docs/reference/calc_allele_LLR.html
docs/reference/calc_allele_lik.html
docs/reference/calc_cluster_dist.html
docs/reference/calc_exp_LLR.html
docs/reference/calc_phi_mle_lnpois.html
docs/reference/calc_trans_mat.html
docs/reference/check_allele_df.html
docs/reference/check_exp_ref.html
docs/reference/check_matrix.html
docs/reference/choose_ref_cor.html
docs/reference/classify_alleles.html
docs/reference/combine_bulk.html
docs/reference/compute_posterior.html
docs/reference/contract_nodes.html
docs/reference/dbbinom.html
docs/reference/detect_clonal_loh.html
docs/reference/dpoilog.html
docs/reference/exp_hclust.html
docs/reference/expand_states.html
docs/reference/fill_neu_segs.html
docs/reference/filter_genes.html
docs/reference/find_common_diploid.html
docs/reference/fit_bbinom.html
docs/reference/fit_gamma.html
docs/reference/fit_gpois.html
docs/reference/fit_lnpois.html
docs/reference/fit_ref_sse.html
docs/reference/forward_back_allele.html
docs/reference/genotype.html
docs/reference/get_allele_bulk.html
docs/reference/get_allele_hmm.html
docs/reference/get_allele_post.html
docs/reference/get_bulk.html
docs/reference/get_clone_post.html
docs/reference/get_exp_bulk.html
docs/reference/get_exp_likelihoods.html
docs/reference/get_exp_post.html
docs/reference/get_exp_sc.html
docs/reference/get_haplotype_post.html
docs/reference/get_internal_nodes.html
docs/reference/get_joint_post.html
docs/reference/get_lambdas_bar.html
docs/reference/get_move_cost.html
docs/reference/get_move_opt.html
docs/reference/get_mut_tree.html
docs/reference/get_nodes_celltree.html
docs/reference/get_segs_consensus.html
docs/reference/get_segs_neu.html
docs/reference/get_snps.html
docs/reference/get_trans_probs.html
docs/reference/get_tree_post.html
docs/reference/index.html
docs/reference/l_bbinom.html
docs/reference/l_gpois.html
docs/reference/l_lnpois.html
docs/reference/l_s_v.html
docs/reference/label_edges.html
docs/reference/label_genotype.html
docs/reference/ladderize.html
docs/reference/likelihood_joint.html
docs/reference/make_group_bulks.html
docs/reference/mark_tumor_lineage.html
docs/reference/mut_to_tree.html
docs/reference/nni.html
docs/reference/nnin.html
docs/reference/perform_nni.html
docs/reference/phi_hat_roll.html
docs/reference/phi_hat_seg.html
docs/reference/plot_bulks.html
docs/reference/plot_consensus.html
docs/reference/plot_exp_roll.html
docs/reference/plot_mut_history.html
docs/reference/plot_phylo_heatmap.html
docs/reference/plot_psbulk.html
docs/reference/plot_sc_tree.html
docs/reference/pnorm.range.log.html
docs/reference/preprocess_allele.html
docs/reference/resolve_cnvs.html
docs/reference/retest_bulks.html
docs/reference/retest_cnv.html
docs/reference/run_allele_hmm.html
docs/reference/run_group_hmms.html
docs/reference/run_joint_hmm.html
docs/reference/run_numbat.html
docs/reference/score_mut.html
docs/reference/score_mut_helper.html
docs/reference/score_tree.html
docs/reference/simes_p.html
docs/reference/simplify_history.html
docs/reference/smooth_expression.html
docs/reference/smooth_segs.html
docs/reference/switch_prob_cm.html
docs/reference/test_multi_allelic.html
docs/reference/theta_hat_roll.html
docs/reference/theta_hat_seg.html
docs/reference/to_phylo.html
docs/reference/transfer_links.html
docs/reference/viterbi_allele.html
docs/reference/viterbi_joint.html
docs/reference/viterbi_loh.html
docs/search.json
docs/sitemap.xml
inst/CITATION
inst/bin/pileup_and_phase.R
logo.png
man/Modes.Rd
man/Numbat.Rd
man/acen_hg19.Rd
man/acen_hg38.Rd
man/aggregate_counts.Rd
man/analyze_bulk.Rd
man/annot_consensus.Rd
man/annot_haplo_segs.Rd
man/annot_ref.Rd
man/annot_segs.Rd
man/annot_superclones.Rd
man/annot_theta_roll.Rd
man/approx_phi_post.Rd
man/approx_theta_post.Rd
man/binary_entropy.Rd
man/bulk_example.Rd
man/calc_allele_LLR.Rd
man/calc_allele_lik.Rd
man/calc_cluster_dist.Rd
man/calc_exp_LLR.Rd
man/calc_phi_mle_lnpois.Rd
man/calc_trans_mat.Rd
man/check_allele_df.Rd
man/check_exp_ref.Rd
man/check_matrix.Rd
man/choose_ref_cor.Rd
man/chrom_sizes_hg19.Rd
man/chrom_sizes_hg38.Rd
man/classify_alleles.Rd
man/cnv_heatmap.Rd
man/combine_bulk.Rd
man/compute_posterior.Rd
man/contract_nodes.Rd
man/count_mat_example.Rd
man/count_mat_ref.Rd
man/dbbinom.Rd
man/detect_clonal_loh.Rd
man/df_allele_example.Rd
man/dpoilog.Rd
man/exp_hclust.Rd
man/expand_states.Rd
man/fill_neu_segs.Rd
man/filter_genes.Rd
man/find_common_diploid.Rd
man/fit_bbinom.Rd
man/fit_gamma.Rd
man/fit_gpois.Rd
man/fit_lnpois.Rd
man/fit_ref_sse.Rd
man/forward_back_allele.Rd
man/gaps_hg19.Rd
man/gaps_hg38.Rd
man/genotype.Rd
man/get_allele_bulk.Rd
man/get_allele_hmm.Rd
man/get_allele_post.Rd
man/get_bulk.Rd
man/get_clone_post.Rd
man/get_exp_bulk.Rd
man/get_exp_likelihoods.Rd
man/get_exp_post.Rd
man/get_exp_sc.Rd
man/get_haplotype_post.Rd
man/get_internal_nodes.Rd
man/get_joint_post.Rd
man/get_lambdas_bar.Rd
man/get_move_cost.Rd
man/get_move_opt.Rd
man/get_mut_tree.Rd
man/get_nodes_celltree.Rd
man/get_segs_consensus.Rd
man/get_segs_neu.Rd
man/get_snps.Rd
man/get_trans_probs.Rd
man/get_tree_post.Rd
man/gexp_roll_example.Rd
man/gtf_hg19.Rd
man/gtf_hg38.Rd
man/hc_example.Rd
man/joint_post_example.Rd
man/l_bbinom.Rd
man/l_gpois.Rd
man/l_lnpois.Rd
man/l_s_v.Rd
man/label_edges.Rd
man/label_genotype.Rd
man/ladderize.Rd
man/make_group_bulks.Rd
man/mark_tumor_lineage.Rd
man/mut_graph_example.Rd
man/mut_to_tree.Rd
man/nni.Rd
man/nnin.Rd
man/perform_nni.Rd
man/phi_hat_roll.Rd
man/phi_hat_seg.Rd
man/phylogeny_example.Rd
man/plot_bulks.Rd
man/plot_consensus.Rd
man/plot_exp_roll.Rd
man/plot_mut_history.Rd
man/plot_phylo_heatmap.Rd
man/plot_psbulk.Rd
man/plot_sc_tree.Rd
man/pnorm.range.log.Rd
man/pre_likelihood_hmm.Rd
man/preprocess_allele.Rd
man/ref_hca.Rd
man/ref_hca_counts.Rd
man/resolve_cnvs.Rd
man/retest_bulks.Rd
man/retest_cnv.Rd
man/run_allele_hmm.Rd
man/run_group_hmms.Rd
man/run_joint_hmm.Rd
man/run_numbat.Rd
man/score_mut.Rd
man/score_mut_helper.Rd
man/score_tree.Rd
man/segs_example.Rd
man/simes_p.Rd
man/simplify_history.Rd
man/smooth_expression.Rd
man/smooth_segs.Rd
man/switch_prob_cm.Rd
man/test_multi_allelic.Rd
man/theta_hat_roll.Rd
man/theta_hat_seg.Rd
man/to_phylo.Rd
man/transfer_links.Rd
man/upgma.Rd
man/vcf_meta.Rd
man/viterbi_allele.Rd
man/viterbi_joint.Rd
man/viterbi_loh.Rd
numbat.png
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
src/Makevars
src/Makevars.win
src/RcppExports.cpp
src/bbinom.cpp
src/hmm.cpp
src/mle.cpp
src/phylogeny.cpp
src/poilog.cpp
tests/testthat.R
tests/testthat/test_functions.R
vignettes/numbat.Rmd
vignettes/results.Rmd
