broadinstitute/infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq Data

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Search the broadinstitute/infercnv package
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Functions
204
Source code
73
Man pages
21
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broadinstitute/infercnv: Infer Copy Number Variation from Single-Cell RNA-Seq Data
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API for broadinstitute/infercnv
Infer Copy Number Variation from Single-Cell RNA-Seq Data

Global functions
.apply_dropout Source code
.apply_logistic_val_adj Source code
.below_min_mean_expr_cutoff Source code
.build_and_add_hspike Source code
.call.FUN Source code
.center_columns Source code
.clear_noise Source code
.compare_args Source code
.compare_obs_vs_fit_sc_cnv_sd Source code
.define_cnv_gene_regions Source code
.estimateSingleCellParamsSplatterScrape Source code
.estimate_common_dispersion Source code
.find_DE_stat_significance Source code
.getLNormFactors Source code
.get_HMM Source code
.get_average_bounds Source code
.get_cnv_gene_region_bounds Source code
.get_features Source code
.get_gene_expr_by_cnv Source code
.get_gene_expr_mean_sd_by_cnv Source code
.get_hspike_chr_info Source code
.get_logistic_params Source code
.get_mean_var_given_matrix Source code
.get_mean_var_table Source code
.get_mean_vs_p0_from_matrix Source code
.get_mean_vs_p0_table Source code
.get_mean_vs_p0_table_from_matrix Source code
.get_normal_gene_mean_bounds Source code
.get_relevant_args_list Source code
.get_simulated_cell_matrix Source code
.get_simulated_cell_matrix_using_meanvar_trend Source code
.get_simulated_cell_matrix_using_meanvar_trend_given_normal_matr Source code
.get_simulated_cell_matrix_using_meanvar_trend_helper Source code
.get_state_consensus Source code
.get_state_emission_params Source code
.get_top_n_regions Source code
.get_tree_height_via_ecdf Source code Source code
.i3HMM_get_HMM Source code
.i3HMM_get_sd_trend_by_num_cells_fit Source code
.invalid Source code
.is.grouped Source code
.leiden_seurat_preprocess_routine Source code
.leiden_simple_snn Source code
.logistic Source code
.logistic_midpt_slope Source code
.mask_DE_genes Source code
.mean_vs_p0_to_stats Source code
.median_filter Source code
.normalize_data_matrix_by_seq_depth Source code
.order_reduce Source code
.pairwise_dendrogram Source code
.parameterize_random_cluster_heights Source code
.parameterize_random_cluster_heights_smoothed_trees Source code
.partition_by_random_smoothed_trees Source code
.partition_by_random_trees Source code
.plot.text Source code
.plot_cnv_mean_sd_for_num_cells Source code
.plot_cnv_observations Source code
.plot_cnv_references Source code
.plot_gene_expr_by_cnv Source code
.plot_observations_layout Source code
.plot_tree_height_dist Source code Source code
.redo_hierarchical_clustering Source code
.remove_outliers_norm Source code
.remove_tails Source code
.scale.data Source code
.scale.x Source code
.sim_expr_val Source code
.sim_expr_val_mean_var Source code
.sim_expr_val_mean_var_no_dropout Source code
.sim_foreground Source code
.simulateSingleCellCountsMatrixSplatterScrape Source code
.single_element_dendrogram Source code
.single_tumor_leiden_subclustering Source code
.single_tumor_subclustering Source code
.single_tumor_subclustering_recursive_random_smoothed_trees Source code
.single_tumor_subclustering_recursive_random_trees Source code
.single_tumor_subclustering_smoothed_tree Source code
.smooth_center_helper Source code
.smooth_helper Source code
.smooth_helper_by_coordinates Source code
.smooth_window Source code
.smooth_window_by_coordinates Source code
.splatEstBCV Source code
.splatEstDropout Source code
.splatEstLib Source code
.splatEstMean Source code
.splatEstOutlier Source code
.splatSimBCVMeans Source code
.splatSimBatchCellMeans Source code
.splatSimDropout Source code
.splatSimGeneMeans Source code
.splatSimLibSizes Source code
.splatSimSingleCellMeans Source code
.splatSimTrueCounts Source code
.subtract_expr Source code
.whole_dataset_leiden_subclustering_per_chr Source code
.winsorize Source code
CreateInfercnvObject Man page Source code
HMM_states Man page
KS_plot Source code
MCMC_inferCNV Man page
MCMC_inferCNV-class Man page
_PACKAGE Man page
add_pseudocount Source code
add_single_branch_to_phylo Source code
add_to_seurat Man page Source code
adjust_genes_regions_report Source code
anscombe_transform Source code
apply_max_threshold_bounds Source code
apply_median_filtering Man page Source code
assign_HMM_states_to_proxy_expr_vals Source code
cell_prob Source code
center_cell_expr_across_chromosome Source code
clear_noise Source code
clear_noise_via_ref_mean_sd Source code
cnv_prob Source code
color.palette Man page Source code
compareNA Source code
create_sep_list Source code
cross_cell_normalize Source code
define_signif_tumor_subclusters Source code
define_signif_tumor_subclusters_via_random_smooothed_trees Source code
depress_log_signal_midpt_val Source code
depress_low_signal_midpt_ratio Source code
determine_mean_delta_via_Z Source code
filterHighPNormals Man page Source code
find_DE_stat_significance Source code
gdist Source code
generate_cnv_region_reports Source code
get.sep Source code
get_DE_genes_basic Source code
get_DE_genes_via_Seurat Source code
get_HoneyBADGER_setGexpDev Source code
get_cell_name_by_grouping Source code
get_group_color_palette Source code
get_hspike_cnv_mean_sd_trend_by_num_cells_fit Source code
get_predicted_CNV_regions Source code
get_reference_grouped_cell_indices Source code
get_spike_dists Source code
has_reference_cells Source code
heatmap.cnv Source code
i3HMM_assign_HMM_states_to_proxy_expr_vals Source code
i3HMM_predict_CNV_via_HMM_on_indiv_cells Source code
i3HMM_predict_CNV_via_HMM_on_tumor_subclusters Source code
i3HMM_predict_CNV_via_HMM_on_whole_tumor_samples Source code
inferCNVBayesNet Man page Source code
infercnv Man page
infercnv-class Man page
infercnv-package Man page
infercnv_annots_example Man page
infercnv_data_example Man page
infercnv_genes_example Man page
infercnv_object_example Man page
invert_log2 Source code
invert_log2xplus1 Source code
log2xplus1 Source code
make_filename Source code
make_zero_NA Source code
mask_non_DE_genes_basic Source code
mask_non_DE_genes_via_Seurat Source code
mcmc_obj Man page
mean_center_gene_expr Source code
normalize_counts_by_seq_depth Source code
plot_cell_prob Source code
plot_cnv Man page Source code
plot_cnv_prob Source code
plot_per_group Man page Source code
plot_subclusters Man page Source code
predict_CNV_via_HMM_on_indiv_cells Source code
predict_CNV_via_HMM_on_tumor_subclusters Source code
predict_CNV_via_HMM_on_tumor_subclusters_per_chr Source code
predict_CNV_via_HMM_on_whole_tumor_samples Source code
remove_genes Source code
remove_genes_at_ends_of_chromosomes Source code
remove_outliers_norm Source code
require_above_min_cells_ref Source code
require_above_min_mean_expr_cutoff Source code
run Man page Source code
run_gibb_sampling Source code
sample_object Man page Source code
scale_infercnv_expr Source code
seurat_from_infercnv_obj Source code
smooth_by_chromosome Source code
smooth_by_chromosome_coordinates Source code
smooth_by_chromosome_runmeans Source code
split_references Source code
subtract_ref_expr_from_obs Source code
transform_to_reference_based_Zscores Source code
validate_infercnv_obj Man page Source code
broadinstitute/infercnv documentation built on Feb. 2, 2025, 11:16 p.m.

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