Index

A

absolute_clonal() (in module cnvlib.call) absolute_dataframe() (in module cnvlib.call) absolute_expect() (in module cnvlib.call) absolute_pure() (in module cnvlib.call) absolute_reference() (in module cnvlib.call) absolute_threshold() (in module cnvlib.call) add() (skgenome.gary.GenomicArray method) add_columns() (skgenome.gary.GenomicArray method) aggregate_gene_counts() (in module cnvlib.import_rna) aggregate_rsem() (in module cnvlib.import_rna) align_gene_info_to_samples() (in module cnvlib.rna)

ampdel() (in module cnvlib.segfilters) apply_weights() (in module cnvlib.fix) as_columns() (skgenome.gary.GenomicArray method) as_dataframe() (skgenome.gary.GenomicArray method) as_rows() (skgenome.gary.GenomicArray method) as_series() (skgenome.gary.GenomicArray method) assert_equal() (in module cnvlib.core) assign_ci_start_end() (in module cnvlib.export) attach_gene_info_to_cnr() (in module cnvlib.rna) autosomes() (skgenome.gary.GenomicArray method) average_depth() (in module cnvlib.autobin)

B

baf_by_ranges() (cnvlib.vary.VariantArray method) bam_total_reads() (in module cnvlib.samutil) batch_make_reference() (in module cnvlib.batch) batch_run_sample() (in module cnvlib.batch) batch_write_coverage() (in module cnvlib.batch) bc_chromosome_draw_label() (in module cnvlib.diagram) bc_organism_draw() (in module cnvlib.diagram) bed2probes() (in module cnvlib.reference) bedcov() (in module cnvlib.coverage) before() (in module cnvlib.rna)

bias_correct_logr() (in module cnvlib.reference) bic() (in module cnvlib.segfilters) biweight_location() (in module cnvlib.descriptives) biweight_midvariance() (in module cnvlib.descriptives) build_chrom_diagram() (in module cnvlib.diagram) by_arm() (skgenome.gary.GenomicArray method) by_chromosome() (skgenome.gary.GenomicArray method) by_gene() (cnvlib.cnary.CopyNumArray method) by_ranges() (in module skgenome.intersect) (skgenome.gary.GenomicArray method) by_shared_chroms() (in module skgenome.intersect)

C

calc_intervals() (in module cnvlib.segmetrics) calculate_gc_lo() (in module cnvlib.reference) call_quiet() (in module cnvlib.core) center_all() (cnvlib.cnary.CopyNumArray method) center_by_window() (in module cnvlib.fix) check_inputs() (in module cnvlib.smoothing) check_unique() (in module cnvlib.core) choose_segment_color() (in module cnvlib.scatter) chromosome() (skgenome.gary.GenomicArray property) (skgenome.rangelabel.NamedRegion property) (skgenome.rangelabel.Region property) chromosome_scatter() (in module cnvlib.scatter) chromosome_sizes() (in module cnvlib.plots) ci() (in module cnvlib.segfilters) cn() (in module cnvlib.segfilters) cnv_on_chromosome() (in module cnvlib.scatter) cnv_on_genome() (in module cnvlib.scatter) cnvlib module cnvlib.access module cnvlib.antitarget module cnvlib.autobin module cnvlib.batch module cnvlib.call module cnvlib.cmdutil module cnvlib.cnary module cnvlib.commands module cnvlib.core module cnvlib.coverage module cnvlib.descriptives module cnvlib.diagram module cnvlib.export module cnvlib.fix module cnvlib.heatmap module

cnvlib.import_rna module cnvlib.importers module cnvlib.metrics module cnvlib.parallel module cnvlib.params module cnvlib.plots module cnvlib.reference module cnvlib.reports module cnvlib.rna module cnvlib.samutil module cnvlib.scatter module cnvlib.segfilters module cnvlib.segmentation module cnvlib.segmetrics module cnvlib.smoothing module cnvlib.target module cnvlib.vary module combine_probes() (in module cnvlib.reference) compare_chrom_names() (in module cnvlib.antitarget) compare_sex_chromosomes() (cnvlib.cnary.CopyNumArray method) concat() (skgenome.gary.GenomicArray method) confidence_interval_bootstrap() (in module cnvlib.segmetrics) convolve_unweighted() (in module cnvlib.smoothing) convolve_weighted() (in module cnvlib.smoothing) coords() (skgenome.gary.GenomicArray method) copy() (skgenome.gary.GenomicArray method) CopyNumArray (class in cnvlib.cnary) correct_cnr() (in module cnvlib.rna) create_clusters() (in module cnvlib.reference) create_diagram() (in module cnvlib.diagram) cut() (skgenome.gary.GenomicArray method) cvg2rgb() (in module cnvlib.plots)

D

dedupe_ens_hugo() (in module cnvlib.rna) dedupe_ens_no_hugo() (in module cnvlib.rna) dedupe_tx() (in module cnvlib.rna) detect_bedcov_columns() (in module cnvlib.coverage) detect_big_chroms() (in module skgenome.chromsort) do_access() (in module cnvlib.access) (in module cnvlib.commands) do_antitarget() (in module cnvlib.antitarget) (in module cnvlib.commands) do_autobin() (in module cnvlib.autobin) (in module cnvlib.commands) do_bintest() (in module cnvlib.commands) do_breaks() (in module cnvlib.commands) (in module cnvlib.reports) do_call() (in module cnvlib.call) (in module cnvlib.commands) do_coverage() (in module cnvlib.commands) (in module cnvlib.coverage) do_fix() (in module cnvlib.commands) (in module cnvlib.fix) do_genemetrics() (in module cnvlib.commands) (in module cnvlib.reports) do_heatmap() (in module cnvlib.commands) (in module cnvlib.heatmap)

do_import_picard() (in module cnvlib.importers) do_import_rna() (in module cnvlib.commands) (in module cnvlib.import_rna) do_import_theta() (in module cnvlib.commands) (in module cnvlib.importers) do_metrics() (in module cnvlib.commands) (in module cnvlib.metrics) do_reference() (in module cnvlib.commands) (in module cnvlib.reference) do_reference_flat() (in module cnvlib.commands) (in module cnvlib.reference) do_scatter() (in module cnvlib.commands) (in module cnvlib.scatter) do_segmentation() (in module cnvlib.commands) (in module cnvlib.segmentation) do_segmetrics() (in module cnvlib.commands) (in module cnvlib.segmetrics) do_sex() (in module cnvlib.commands) do_target() (in module cnvlib.commands) (in module cnvlib.target) drop_extra_columns() (skgenome.gary.GenomicArray method) drop_low_coverage() (cnvlib.cnary.CopyNumArray method) drop_noncanonical_contigs() (in module cnvlib.access) (in module cnvlib.antitarget) drop_outliers() (in module cnvlib.segmentation)

E

edge_gains() (in module cnvlib.fix) edge_losses() (in module cnvlib.fix) end() (skgenome.gary.GenomicArray property) (skgenome.rangelabel.NamedRegion property) (skgenome.rangelabel.Region property) ensure_bam_index() (in module cnvlib.samutil) ensure_bam_sorted() (in module cnvlib.samutil) ensure_path() (in module cnvlib.core) enumerate_changes() (in module cnvlib.segfilters)

ests_of_scale() (in module cnvlib.metrics) expect_flat_log2() (cnvlib.cnary.CopyNumArray method) export_bed() (in module cnvlib.export) export_gistic_markers() (in module cnvlib.export) export_nexus_basic() (in module cnvlib.export) export_nexus_ogt() (in module cnvlib.export) export_seg() (in module cnvlib.export) export_theta() (in module cnvlib.export) export_theta_snps() (in module cnvlib.export) export_vcf() (in module cnvlib.export)

F

fasta_extract_regions() (in module cnvlib.reference) fbase() (in module cnvlib.core) filter() (skgenome.gary.GenomicArray method) filter_names() (in module cnvlib.target) filter_probes() (in module cnvlib.rna) first_of() (in module skgenome.combiners) flatten() (in module skgenome.merge) (skgenome.gary.GenomicArray method)

fmt_cdt() (in module cnvlib.export) fmt_gct() (in module cnvlib.export) fmt_jtv() (in module cnvlib.export) from_columns() (skgenome.gary.GenomicArray class method) from_label() (in module skgenome.rangelabel) from_rows() (skgenome.gary.GenomicArray class method)

G

gapper_scale() (in module cnvlib.descriptives) gene() (skgenome.rangelabel.NamedRegion property) gene_coords_by_name() (in module cnvlib.plots) gene_coords_by_range() (in module cnvlib.plots) gene_metrics_by_gene() (in module cnvlib.reports) gene_metrics_by_segment() (in module cnvlib.reports) genome_scatter() (in module cnvlib.scatter) GenomicArray (class in skgenome.gary) get_antitargets() (in module cnvlib.antitarget) get_breakpoints() (in module cnvlib.reports) get_combiners() (in module skgenome.combiners)

get_edge_bias() (in module cnvlib.fix) get_fasta_stats() (in module cnvlib.reference) get_filename() (in module skgenome.tabio) get_gene_intervals() (in module cnvlib.reports) get_read_length() (in module cnvlib.samutil) get_regions() (in module cnvlib.access) get_repeat_slices() (in module cnvlib.plots) get_segment_vafs() (in module cnvlib.scatter) group_by_genes() (in module cnvlib.reports) guess_chromosome_regions() (in module cnvlib.antitarget) guess_window_size() (in module cnvlib.smoothing) guess_xx() (cnvlib.cnary.CopyNumArray method)

H

het_frac_by_ranges() (cnvlib.vary.VariantArray method) heterozygous() (cnvlib.vary.VariantArray method)

highlight_genes() (in module cnvlib.scatter) hybrid() (in module cnvlib.autobin)

I

idx_ranges() (in module skgenome.intersect) idxstats() (in module cnvlib.samutil) idxstats2ga() (in module cnvlib.autobin) in_range() (skgenome.gary.GenomicArray method) in_ranges() (skgenome.gary.GenomicArray method) infer_sexes() (in module cnvlib.reference) interquartile_range() (in module cnvlib.descriptives) intersection() (skgenome.gary.GenomicArray method) interval_coverages() (in module cnvlib.coverage)

interval_coverages_count() (in module cnvlib.coverage) interval_coverages_pileup() (in module cnvlib.coverage) into_ranges() (in module skgenome.intersect) (skgenome.gary.GenomicArray method) is_canonical_contig_name() (in module cnvlib.antitarget) is_newer_than() (in module cnvlib.samutil) iter_ranges() (in module skgenome.intersect) iter_ranges_of() (skgenome.gary.GenomicArray method) iter_slices() (in module skgenome.intersect)

J

join_regions() (in module cnvlib.access)

join_strings() (in module skgenome.combiners)

K

kaiser() (in module cnvlib.smoothing)

keep_columns() (skgenome.gary.GenomicArray method)

L

labels() (skgenome.gary.GenomicArray method) last_of() (in module skgenome.combiners) load_adjust_coverages() (in module cnvlib.fix) load_cnv_expression_corr() (in module cnvlib.rna) load_gene_info() (in module cnvlib.rna)

load_het_snps() (in module cnvlib.cmdutil) load_sample_block() (in module cnvlib.reference) locate_entrez_dupes() (in module cnvlib.rna) log2() (cnvlib.cnary.CopyNumArray property) log2_ratios() (in module cnvlib.call) log_this() (in module cnvlib.access)

M

make_ci_func() (in module cnvlib.segmetrics) make_const() (in module skgenome.combiners) make_pi_func() (in module cnvlib.segmetrics) map() (cnvlib.parallel.SerialPool method) mask_bad_bins() (in module cnvlib.fix) match_ref_to_sample() (in module cnvlib.fix) mean_squared_error() (in module cnvlib.descriptives) median_absolute_deviation() (in module cnvlib.descriptives) merge() (in module skgenome.merge) (skgenome.gary.GenomicArray method) merge_samples() (in module cnvlib.export) merge_strands() (in module skgenome.combiners) midsize_file() (in module cnvlib.autobin) mirrored_baf() (cnvlib.vary.VariantArray method) modal_location() (in module cnvlib.descriptives) module cnvlib cnvlib.access cnvlib.antitarget cnvlib.autobin cnvlib.batch cnvlib.call cnvlib.cmdutil cnvlib.cnary cnvlib.commands cnvlib.core cnvlib.coverage cnvlib.descriptives cnvlib.diagram cnvlib.export cnvlib.fix cnvlib.heatmap cnvlib.import_rna cnvlib.importers cnvlib.metrics cnvlib.parallel cnvlib.params cnvlib.plots cnvlib.reference cnvlib.reports cnvlib.rna cnvlib.samutil cnvlib.scatter cnvlib.segfilters cnvlib.segmentation cnvlib.segmetrics cnvlib.smoothing cnvlib.target cnvlib.vary skgenome skgenome.chromsort skgenome.combiners skgenome.gary skgenome.intersect skgenome.merge skgenome.rangelabel skgenome.subdivide skgenome.subtract skgenome.tabio

N

NamedRegion (class in skgenome.rangelabel)

normalize_read_depths() (in module cnvlib.rna)

O

on_array() (in module cnvlib.descriptives) on_weighted_array() (in module cnvlib.descriptives)

outlier_iqr() (in module cnvlib.smoothing) outlier_mad_median() (in module cnvlib.smoothing)

P

parse_theta_results() (in module cnvlib.importers)

pick_pool() (in module cnvlib.parallel) plot_x_dividers() (in module cnvlib.plots)

Q

q_n() (in module cnvlib.descriptives)

R

read() (in module skgenome.tabio) read_auto() (in module skgenome.tabio) read_cna() (in module cnvlib.cmdutil) ref_means_nbins() (in module cnvlib.export) reference2regions() (in module cnvlib.reference) Region (class in skgenome.rangelabel) region_depth_count() (in module cnvlib.coverage) region_size_by_chrom() (in module cnvlib.autobin) require_column() (in module cnvlib.segfilters) rescale_baf() (in module cnvlib.call)

residuals() (cnvlib.cnary.CopyNumArray method) resize_ranges() (skgenome.gary.GenomicArray method) result() (cnvlib.parallel.SerialFuture method) rm() (in module cnvlib.parallel) rolling_median() (in module cnvlib.smoothing) rolling_outlier_iqr() (in module cnvlib.smoothing) rolling_outlier_quantile() (in module cnvlib.smoothing) rolling_outlier_std() (in module cnvlib.smoothing) rolling_quantile() (in module cnvlib.smoothing) rolling_std() (in module cnvlib.smoothing)

S

safe_log2() (in module cnvlib.rna) safe_write() (in module skgenome.tabio) sample_id() (skgenome.gary.GenomicArray property) sample_midsize_regions() (in module cnvlib.autobin) sample_region_cov() (in module cnvlib.autobin) savgol() (in module cnvlib.smoothing) segment_mean() (in module cnvlib.segmetrics) segments2vcf() (in module cnvlib.export) select_range_genes() (in module cnvlib.scatter) sem() (in module cnvlib.segfilters) SerialFuture (class in cnvlib.parallel) SerialPool (class in cnvlib.parallel) set_colorbar() (in module cnvlib.heatmap) set_xlim_from() (in module cnvlib.scatter) setup_chromosome() (in module cnvlib.scatter) shared_chroms() (in module cnvlib.autobin) shift_sex_chroms() (in module cnvlib.reference) shift_xx() (cnvlib.cnary.CopyNumArray method) shorten_labels() (in module cnvlib.target) shortest_name() (in module cnvlib.target) shuffle() (skgenome.gary.GenomicArray method) shutdown() (cnvlib.parallel.SerialPool method) skgenome module skgenome.chromsort module skgenome.combiners module skgenome.gary module skgenome.intersect module

skgenome.merge module skgenome.rangelabel module skgenome.subdivide module skgenome.subtract module skgenome.tabio module smooth_log2() (cnvlib.cnary.CopyNumArray method) sniff_region_format() (in module skgenome.tabio) snv_on_chromosome() (in module cnvlib.scatter) snv_on_genome() (in module cnvlib.scatter) sort() (skgenome.gary.GenomicArray method) sort_columns() (skgenome.gary.GenomicArray method) sorter_chrom() (in module skgenome.chromsort) squash() (skgenome.gary.GenomicArray method) squash_by_groups() (in module cnvlib.segfilters) squash_genes() (cnvlib.cnary.CopyNumArray method) squash_region() (in module cnvlib.segfilters) start() (skgenome.gary.GenomicArray property) (skgenome.rangelabel.NamedRegion property) (skgenome.rangelabel.Region property) subdivide() (in module skgenome.subdivide) (skgenome.gary.GenomicArray method) submit() (cnvlib.parallel.SerialPool method) subtract() (in module skgenome.subtract) (skgenome.gary.GenomicArray method) summarize_info() (in module cnvlib.reference)

T

temp_write_text() (in module cnvlib.core) theta_read_counts() (in module cnvlib.export) to_chunks() (in module cnvlib.parallel) to_label() (in module skgenome.rangelabel) total_range_size() (skgenome.gary.GenomicArray method)

total_region_size() (in module cnvlib.autobin) transfer_fields() (in module cnvlib.segmentation) translate_region_to_bins() (in module cnvlib.plots) translate_segments_to_bins() (in module cnvlib.plots) tsl2int() (in module cnvlib.rna) tumor_boost() (cnvlib.vary.VariantArray method)

U

unpack_range() (in module skgenome.rangelabel) unpipe_name() (in module cnvlib.importers)

update_binwise_positions() (in module cnvlib.plots) update_binwise_positions_simple() (in module cnvlib.plots) update_chrom_length() (in module cnvlib.autobin)

V

VariantArray (class in cnvlib.vary)

venn() (in module skgenome.intersect) verify_sample_sex() (in module cnvlib.cmdutil)

W

warn_bad_bins() (in module cnvlib.reference) weighted_mad() (in module cnvlib.descriptives) weighted_median() (in module cnvlib.descriptives) weighted_std() (in module cnvlib.descriptives)

write() (in module skgenome.tabio) write_dataframe() (in module cnvlib.cmdutil) write_text() (in module cnvlib.cmdutil) write_tsv() (in module cnvlib.cmdutil)

Z

zip_repeater() (in module cnvlib.metrics)

zygosity_from_freq() (cnvlib.vary.VariantArray method)