CNVkit
v0.9.3
Quick start
Copy number calling pipeline
Plots and graphics
Text and tabular reports
Compatibility and other I/O
RNA expression
Additional scripts
File formats
Chromosomal sex
Calling copy number gains and losses
Allele frequencies and copy number
Bias corrections
Tumor analysis
Tumor heterogeneity
Germline analysis
Whole-genome sequencing and targeted amplicon capture
cnvlib package
scikit-genome package
CNVkit
Docs
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Index
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C
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O
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P
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Q
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R
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S
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T
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U
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V
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W
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Z
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)
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)
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
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 attribute)
(skgenome.rangelabel.NamedRegion attribute)
(skgenome.rangelabel.Region attribute)
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_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_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)
,
[1]
(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)
,
[1]
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 attribute)
(skgenome.rangelabel.NamedRegion attribute)
(skgenome.rangelabel.Region attribute)
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 attribute)
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
heterozygous() (cnvlib.vary.VariantArray method)
highlight_genes() (in module cnvlib.scatter)
hybrid() (in module cnvlib.autobin)
I
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)
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)
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)
locate_entrez_dupes() (in module cnvlib.rna)
log2 (cnvlib.cnary.CopyNumArray attribute)
log2_ratios() (in module cnvlib.call)
log_this() (in module cnvlib.access)
M
make_const() (in module skgenome.combiners)
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)
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)
prediction_interval() (in module cnvlib.segmetrics)
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)
repair_segments() (in module cnvlib.segmentation)
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 attribute)
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)
segmetric_interval() (in module cnvlib.segmetrics)
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_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)
smoothed() (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 attribute)
(skgenome.rangelabel.NamedRegion attribute)
(skgenome.rangelabel.Region attribute)
subdivide() (in module skgenome.subdivide)
(skgenome.gary.GenomicArray method)
submit() (cnvlib.parallel.SerialPool method)
subtract() (in module skgenome.subtract)
(skgenome.gary.GenomicArray method)
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)
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