CNVkit
v0.7.6
Quick start
Copy number calling pipeline
Plots and graphics
Text and tabular reports
Compatibility and other I/O
Additional scripts
File formats
Bias corrections
Calling absolute copy number
Tumor heterogeneity
Whole-genome sequencing and targeted amplicon capture
Python API (cnvlib package)
CNVkit
Docs
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Index
A
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B
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C
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D
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E
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F
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G
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I
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J
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K
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L
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M
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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
A
absolute_clonal() (in module cnvlib.call)
absolute_dataframe() (in module cnvlib.call)
absolute_pure() (in module cnvlib.call)
absolute_threshold() (in module cnvlib.call)
add() (cnvlib.gary.GenomicArray method)
add_columns() (cnvlib.gary.GenomicArray method)
add_refflat_names() (in module cnvlib.target)
apply_async() (cnvlib.parallel.SerialPool method)
apply_weights() (in module cnvlib.fix)
as_columns() (cnvlib.gary.GenomicArray method)
as_dataframe() (cnvlib.gary.GenomicArray method)
as_rows() (cnvlib.gary.GenomicArray method)
assert_equal() (in module cnvlib.core)
assign_names() (in module cnvlib.target)
autosomes() (cnvlib.gary.GenomicArray method)
B
bam_total_reads() (in module cnvlib.coverage)
batch_make_reference() (in module cnvlib.commands)
batch_run_sample() (in module cnvlib.commands)
batch_write_coverage() (in module cnvlib.commands)
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)
biweight_location() (in module cnvlib.metrics)
biweight_midvariance() (in module cnvlib.metrics)
build_chrom_diagram() (in module cnvlib.diagram)
by_chromosome() (cnvlib.gary.GenomicArray method)
by_gene() (cnvlib.cnary.CopyNumArray method)
by_ranges() (cnvlib.gary.GenomicArray method)
C
calculate_gc_lo() (in module cnvlib.reference)
call_quiet() (in module cnvlib.ngfrills)
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)
chromosome (cnvlib.gary.GenomicArray attribute)
chromosome_sizes() (in module cnvlib.plots)
close() (cnvlib.parallel.SerialPool method)
cnv_on_chromosome() (in module cnvlib.plots)
cnv_on_genome() (in module cnvlib.plots)
cnvlib (module)
cnvlib.antitarget (module)
cnvlib.call (module)
cnvlib.cnary (module)
cnvlib.commands (module)
cnvlib.core (module)
cnvlib.coverage (module)
cnvlib.diagram (module)
cnvlib.export (module)
cnvlib.fix (module)
cnvlib.gary (module)
cnvlib.importers (module)
cnvlib.metrics (module)
cnvlib.ngfrills (module)
cnvlib.parallel (module)
cnvlib.params (module)
cnvlib.plots (module)
cnvlib.rary (module)
cnvlib.reference (module)
cnvlib.reports (module)
cnvlib.segmentation (module)
cnvlib.smoothing (module)
cnvlib.target (module)
cnvlib.vary (module)
combine_probes() (in module cnvlib.reference)
concat() (cnvlib.gary.GenomicArray method)
confidence_interval_bootstrap() (in module cnvlib.metrics)
coords() (cnvlib.gary.GenomicArray method)
copy() (cnvlib.gary.GenomicArray method)
CopyNumArray (class in cnvlib.cnary)
create_chrom_ids() (in module cnvlib.export)
create_diagram() (in module cnvlib.diagram)
csvstring() (in module cnvlib.commands)
cvg2rgb() (in module cnvlib.plots)
D
do_access() (in module cnvlib.commands)
do_antitarget() (in module cnvlib.commands)
do_breaks() (in module cnvlib.commands)
do_call() (in module cnvlib.commands)
do_coverage() (in module cnvlib.commands)
do_fix() (in module cnvlib.commands)
do_gainloss() (in module cnvlib.commands)
do_heatmap() (in module cnvlib.commands)
do_reference() (in module cnvlib.commands)
do_reference_flat() (in module cnvlib.commands)
do_rescale() (in module cnvlib.commands)
do_scatter() (in module cnvlib.commands)
do_segmentation() (in module cnvlib.segmentation)
do_targets() (in module cnvlib.commands)
drop_extra_columns() (cnvlib.gary.GenomicArray method)
drop_low_coverage() (cnvlib.cnary.CopyNumArray method)
drop_outliers() (in module cnvlib.segmentation)
E
edge_gains() (in module cnvlib.fix)
edge_losses() (in module cnvlib.fix)
emit() (in module cnvlib.target)
end (cnvlib.gary.GenomicArray attribute)
ensure_path() (in module cnvlib.ngfrills)
ests_of_scale() (in module cnvlib.metrics)
expect_flat_cvg() (cnvlib.cnary.CopyNumArray method)
export_bed() (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_vcf() (in module cnvlib.export)
F
fbase() (in module cnvlib.core)
filter_names() (in module cnvlib.target)
find_background_regions() (in module cnvlib.antitarget)
find_picard_files() (in module cnvlib.importers)
fit_edges() (in module cnvlib.smoothing)
fmt_cdt() (in module cnvlib.export)
fmt_gct() (in module cnvlib.export)
fmt_jtv() (in module cnvlib.export)
format_theta_row() (in module cnvlib.export)
from_columns() (cnvlib.gary.GenomicArray class method)
from_rows() (cnvlib.gary.GenomicArray class method)
G
gainloss_by_gene() (in module cnvlib.reports)
gainloss_by_segment() (in module cnvlib.reports)
gene_coords_by_name() (in module cnvlib.plots)
gene_coords_by_range() (in module cnvlib.plots)
GenomicArray (class in cnvlib.gary)
get_background() (in module cnvlib.antitarget)
get_breakpoints() (in module cnvlib.reports)
get_edge_bias() (in module cnvlib.fix)
get_fasta_stats() (in module cnvlib.reference)
get_gene_intervals() (in module cnvlib.reports)
get_relative_chrx_cvg() (cnvlib.cnary.CopyNumArray method)
group_by_genes() (in module cnvlib.reports)
group_snvs_by_segments() (in module cnvlib.plots)
guess_average_depth() (cnvlib.cnary.CopyNumArray method)
guess_chromosome_regions() (in module cnvlib.antitarget)
guess_xx() (cnvlib.cnary.CopyNumArray method)
I
import_picard_pertargetcoverage() (in module cnvlib.importers)
import_seg() (in module cnvlib.importers)
in_range() (cnvlib.gary.GenomicArray method)
in_ranges() (cnvlib.gary.GenomicArray method)
interquartile_range() (in module cnvlib.metrics)
interval_coverages() (in module cnvlib.coverage)
interval_coverages_count() (in module cnvlib.coverage)
interval_coverages_pileup() (in module cnvlib.coverage)
J
join() (cnvlib.parallel.SerialPool method)
K
keep_columns() (cnvlib.gary.GenomicArray method)
L
labels() (cnvlib.gary.GenomicArray method)
load_adjust_coverages() (in module cnvlib.fix)
log2 (cnvlib.cnary.CopyNumArray attribute)
M
mask_bad_probes() (in module cnvlib.fix)
match_ref_to_probes() (in module cnvlib.fix)
match_to_bins() (cnvlib.gary.GenomicArray method)
median_absolute_deviation() (in module cnvlib.metrics)
merge_samples() (in module cnvlib.export)
mirrored_baf() (cnvlib.vary.VariantArray method)
modal_location() (in module cnvlib.metrics)
O
outlier_iqr() (in module cnvlib.smoothing)
outlier_mad_median() (in module cnvlib.smoothing)
P
parse_args() (in module cnvlib.commands)
parse_range_text() (in module cnvlib.plots)
parse_refflat_line() (in module cnvlib.target)
parse_theta_results() (in module cnvlib.importers)
partition_by_chrom() (in module cnvlib.plots)
pick_pool() (in module cnvlib.parallel)
plot_x_dividers() (in module cnvlib.plots)
prediction_interval() (in module cnvlib.metrics)
print_version() (in module cnvlib.commands)
Q
q_n() (in module cnvlib.metrics)
R
rbase() (in module cnvlib.core)
read() (cnvlib.gary.GenomicArray class method)
(cnvlib.rary.RegionArray class method)
(in module cnvlib)
read_refflat_genes() (in module cnvlib.target)
read_vcf() (cnvlib.vary.VariantArray class method)
reference2regions() (in module cnvlib.reference)
region_depth_count() (in module cnvlib.coverage)
RegionArray (class in cnvlib.rary)
repair_segments() (in module cnvlib.segmentation)
residuals() (cnvlib.cnary.CopyNumArray method)
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)
round_log2_ratios() (in module cnvlib.call)
row2label() (cnvlib.gary.GenomicArray static method)
S
safe_write() (in module cnvlib.ngfrills)
sample_id (cnvlib.gary.GenomicArray attribute)
seg2cns() (in module cnvlib.segmentation)
segment_mean() (in module cnvlib.metrics)
segments2vcf() (in module cnvlib.export)
select() (cnvlib.gary.GenomicArray method)
SerialPool (class in cnvlib.parallel)
setup_chromosome() (in module cnvlib.plots)
setup_genome() (in module cnvlib.plots)
shift_xx() (cnvlib.cnary.CopyNumArray method)
shorten_labels() (in module cnvlib.target)
shortest_name() (in module cnvlib.target)
shuffle() (cnvlib.gary.GenomicArray method)
smoothed() (in module cnvlib.smoothing)
snv_on_chromosome() (in module cnvlib.plots)
snv_on_genome() (in module cnvlib.plots)
sort() (cnvlib.gary.GenomicArray method)
sort_columns() (cnvlib.gary.GenomicArray method)
sorter_chrom() (in module cnvlib.core)
sorter_chrom_at() (in module cnvlib.core)
split_targets() (in module cnvlib.target)
squash_genes() (cnvlib.cnary.CopyNumArray method)
squash_segments() (in module cnvlib.segmentation)
start (cnvlib.gary.GenomicArray attribute)
T
temp_write_text() (in module cnvlib.ngfrills)
test_loh() (in module cnvlib.plots)
transfer_names_weights() (in module cnvlib.segmentation)
tumor_boost() (cnvlib.vary.VariantArray method)
U
unpack_range() (in module cnvlib.plots)
unpipe_name() (in module cnvlib.importers)
V
VariantArray (class in cnvlib.vary)
verify_gender_arg() (in module cnvlib.commands)
W
warn_bad_probes() (in module cnvlib.reference)
write() (cnvlib.gary.GenomicArray method)
(cnvlib.rary.RegionArray method)
write_dataframe() (in module cnvlib.core)
write_text() (in module cnvlib.core)
write_tsv() (in module cnvlib.core)
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