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numbat  

Haplotype-Aware CNV Analysis from scRNA-Seq
View on CRAN: Click here


Download and install numbat package within the R console
Install from CRAN:
install.packages("numbat")

Install from Github:
library("remotes")
install_github("cran/numbat")

Install by package version:
library("remotes")
install_version("numbat", "1.4.0")



Attach the package and use:
library("numbat")
Maintained by
Teng Gao
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-09-15
Latest Update: 2023-06-17
Description:
A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at . For details on the method please see Gao et al. Nature Biotechnology (2022) .
How to cite:
Teng Gao (2022). numbat: Haplotype-Aware CNV Analysis from scRNA-Seq. R package version 1.4.0, https://cran.r-project.org/web/packages/numbat
Previous versions and publish date:
1.0.2 (2022-09-15 08:10), 1.1.0 (2022-11-29 19:30), 1.2.1 (2023-01-11 01:20), 1.2.2 (2023-02-14 19:20), 1.3.0 (2023-04-02 19:50), 1.3.2-1 (2023-06-17 20:50), 1.3.2 (2023-06-06 18:40)
Other packages that cited numbat R package
View numbat citation profile
Other R packages that numbat depends, imports, suggests or enhances
Functions, R codes and Examples using the numbat R package
Some associated functions: Modes . Numbat . acen_hg19 . acen_hg38 . aggregate_counts . analyze_bulk . annot_consensus . annot_haplo_segs . annot_ref . annot_segs . annot_theta_mle . annot_theta_roll . annotate_genes . approx_phi_post . approx_theta_post . binary_entropy . bulk_example . calc_allele_LLR . calc_allele_lik . calc_cluster_dist . calc_exp_LLR . calc_phi_mle_lnpois . calc_trans_mat . check_allele_df . check_contam . check_exp_noise . check_exp_ref . check_matrix . check_segs_fix . check_segs_loh . choose_ref_cor . chrom_sizes_hg19 . chrom_sizes_hg38 . classify_alleles . cnv_heatmap . combine_bulk . compute_posterior . contract_nodes . count_mat_example . count_mat_ref . dbbinom . detect_clonal_loh . df_allele_example . dgpois . dpoilog . exp_hclust . expand_states . fill_neu_segs . filter_genes . find_common_diploid . fit_bbinom . fit_gamma . fit_gpois . fit_lnpois . fit_ref_sse . fit_snp_rate . forward_back_allele . gaps_hg19 . gaps_hg38 . generate_postfix . genotype . get_allele_bulk . get_allele_hmm . get_allele_post . get_bulk . get_clone_post . get_exp_bulk . get_exp_likelihoods . get_exp_post . get_exp_sc . get_gtree . get_haplotype_post . get_inter_cm . get_internal_nodes . get_joint_post . get_lambdas_bar . get_move_cost . get_move_opt . get_nodes_celltree . get_ordered_tips . get_segs_consensus . get_segs_neu . get_snps . get_trans_probs . get_tree_post . gexp_roll_example . gtf_hg19 . gtf_hg38 . gtf_mm10 . hc_example . joint_post_example . l_bbinom . l_gpois . l_lnpois . label_edges . label_genotype . likelihood_allele . log_mem . log_message . make_group_bulks . mark_tumor_lineage . mut_graph_example . phi_hat_roll . phi_hat_seg . phylogeny_example . plot_bulks . plot_consensus . plot_exp_roll . plot_mut_history . plot_phylo_heatmap . plot_psbulk . plot_sc_tree . pnorm.range.log . pre_likelihood_hmm . preprocess_allele . ref_hca . ref_hca_counts . relevel_chrom . resolve_cnvs . retest_bulks . retest_cnv . return_missing_columns . run_allele_hmm . run_group_hmms . run_joint_hmm . run_numbat . segs_example . simes_p . simplify_history . smooth_expression . smooth_segs . switch_prob_cm . t_test_pval . test_multi_allelic . theta_hat_roll . theta_hat_seg . transfer_links . upgma . vcf_meta . viterbi_allele . viterbi_joint . viterbi_loh . 
Some associated R codes: RcppExports.R . class.R . data.R . diagnostics.R . genotyping.R . hmm.R . main.R . trees.R . utils.R . vis.R . zzz.R .  Full numbat package functions and examples
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