CNVkit
v0.6.1
Quick start
Copy number calling pipeline
Plots and graphics
Text and tabular reports
Compatibility and other I/O
Additional scripts
File formats
Calling gains and losses
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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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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W
A
add_columns() (cnvlib.cnarray.CopyNumArray method)
apply_async() (cnvlib.commands.SerialPool method)
apply_weights() (in module cnvlib.fix)
assert_equal() (in module cnvlib.core)
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_bin() (cnvlib.cnarray.CopyNumArray method)
by_chromosome() (cnvlib.cnarray.CopyNumArray method)
by_gene() (cnvlib.cnarray.CopyNumArray method)
by_segment() (cnvlib.cnarray.CopyNumArray method)
C
calculate_gc_lo() (in module cnvlib.reference)
calculate_theta_fields() (in module cnvlib.export)
call_quiet() (in module cnvlib.ngfrills)
center_all() (cnvlib.cnarray.CopyNumArray method)
center_by_window() (in module cnvlib.fix)
check_inputs() (in module cnvlib.smoothing)
check_unique() (in module cnvlib.core)
chrom (cnvlib.export.ProbeInfo attribute)
chromosome (cnvlib.cnarray.CopyNumArray attribute)
chromosome_sizes() (in module cnvlib.plots)
close() (cnvlib.commands.SerialPool method)
cnvlib (module)
cnvlib.antitarget (module)
cnvlib.cnarray (module)
cnvlib.commands (module)
cnvlib.core (module)
cnvlib.coverage (module)
cnvlib.diagram (module)
cnvlib.export (module)
cnvlib.fix (module)
cnvlib.importers (module)
cnvlib.metrics (module)
cnvlib.ngfrills (module)
cnvlib.params (module)
cnvlib.plots (module)
cnvlib.reference (module)
cnvlib.reports (module)
cnvlib.segmentation (module)
cnvlib.smoothing (module)
combine_probes() (in module cnvlib.reference)
copy() (cnvlib.cnarray.CopyNumArray method)
CopyNumArray (class in cnvlib.cnarray)
coverage (cnvlib.cnarray.CopyNumArray attribute)
create_chrom_ids() (in module cnvlib.export)
create_diagram() (in module cnvlib.diagram)
create_heatmap() (in module cnvlib.commands)
create_loh() (in module cnvlib.commands)
csvstring() (in module cnvlib.commands)
cvg2rgb() (in module cnvlib.plots)
D
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_reference() (in module cnvlib.commands)
do_reference_flat() (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.cnarray.CopyNumArray method)
E
edge_gain() (in module cnvlib.fix)
edge_loss() (in module cnvlib.fix)
end (cnvlib.cnarray.CopyNumArray attribute)
(cnvlib.export.ProbeInfo attribute)
ensure_path() (in module cnvlib.ngfrills)
ests_of_scale() (in module cnvlib.metrics)
expect_flat_cvg() (in module cnvlib.core)
export_bed() (in module cnvlib.export)
export_freebayes() (in module cnvlib.export)
export_nexus_basic() (in module cnvlib.export)
export_seg() (in module cnvlib.export)
export_theta() (in module cnvlib.export)
F
fbase() (in module cnvlib.core)
filter_column() (in module cnvlib.coverage)
filter_read() (in module cnvlib.coverage)
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)
fmt_multi() (in module cnvlib.export)
fmt_vcf() (in module cnvlib.export)
from_array() (cnvlib.cnarray.CopyNumArray class method)
from_columns() (cnvlib.cnarray.CopyNumArray class method)
from_rows() (cnvlib.cnarray.CopyNumArray class method)
G
gainloss_by_gene() (in module cnvlib.reports)
gainloss_by_segment() (in module cnvlib.reports)
gene (cnvlib.cnarray.CopyNumArray attribute)
(cnvlib.export.ProbeInfo attribute)
gene_coords_by_name() (in module cnvlib.plots)
gene_coords_by_range() (in module cnvlib.plots)
get_background() (in module cnvlib.antitarget)
get_breakpoints() (in module cnvlib.reports)
get_fasta_stats() (in module cnvlib.reference)
get_gene_intervals() (in module cnvlib.reports)
get_relative_chrx_cvg() (in module cnvlib.core)
group_by_genes() (in module cnvlib.reports)
group_coords() (in module cnvlib.antitarget)
group_snvs_by_segments() (in module cnvlib.plots)
guess_chr_x() (in module cnvlib.core)
guess_chromosome_regions() (in module cnvlib.antitarget)
guess_xx() (in module cnvlib.core)
I
import_seg() (in module cnvlib.importers)
in_range() (cnvlib.cnarray.CopyNumArray 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.commands.SerialPool method)
L
label (cnvlib.export.ProbeInfo attribute)
labels() (cnvlib.cnarray.CopyNumArray method)
limit() (in module cnvlib.plots)
load_adjust_coverages() (in module cnvlib.fix)
load_targetcoverage_csv() (in module cnvlib.importers)
M
make_edge_sorter() (in module cnvlib.fix)
mask_bad_probes() (in module cnvlib.reference)
match_ref_to_probes() (in module cnvlib.fix)
median_absolute_deviation() (in module cnvlib.metrics)
merge() (cnvlib.cnarray.CopyNumArray method)
merge_rows() (in module cnvlib.export)
merge_samples() (in module cnvlib.export)
O
outlier_iqr() (in module cnvlib.smoothing)
outlier_mad_median() (in module cnvlib.smoothing)
P
parse_args() (in module cnvlib.commands)
parse_range() (in module cnvlib.plots)
parse_theta_results() (in module cnvlib.importers)
parse_tsv() (in module cnvlib.core)
partition_by_chrom() (in module cnvlib.plots)
pick_pool() (in module cnvlib.commands)
plot_chromosome() (in module cnvlib.plots)
plot_genome() (in module cnvlib.plots)
plot_loh() (in module cnvlib.plots)
plot_x_dividers() (in module cnvlib.plots)
print_version() (in module cnvlib.commands)
probe_center() (in module cnvlib.plots)
probe_deviations_from_segments() (in module cnvlib.metrics)
ProbeInfo (class in cnvlib.export)
Q
q_n() (in module cnvlib.metrics)
R
rbase() (in module cnvlib.core)
read() (cnvlib.cnarray.CopyNumArray class method)
(in module cnvlib)
reference2regions() (in module cnvlib.reference)
region_depth_count() (in module cnvlib.coverage)
repair_segments() (in module cnvlib.segmentation)
rolling_median() (in module cnvlib.smoothing)
row2label() (in module cnvlib.cnarray)
row_to_probe_coverage() (in module cnvlib.export)
S
safe_write() (in module cnvlib.ngfrills)
segment_mean() (in module cnvlib.metrics)
segments2bed() (in module cnvlib.export)
segments2freebayes() (in module cnvlib.export)
select() (cnvlib.cnarray.CopyNumArray method)
SerialPool (class in cnvlib.commands)
shift_xx() (in module cnvlib.core)
shuffle() (cnvlib.cnarray.CopyNumArray method)
smooth_genome_coverages() (in module cnvlib.smoothing)
smoothed() (in module cnvlib.smoothing)
sort() (cnvlib.cnarray.CopyNumArray method)
sorter_chrom() (in module cnvlib.core)
sorter_chrom_at() (in module cnvlib.core)
squash_genes() (cnvlib.cnarray.CopyNumArray method)
squash_segments() (in module cnvlib.segmentation)
start (cnvlib.cnarray.CopyNumArray attribute)
(cnvlib.export.ProbeInfo attribute)
T
temp_write_text() (in module cnvlib.ngfrills)
test_loh() (in module cnvlib.plots)
to_array() (cnvlib.cnarray.CopyNumArray method)
to_rows() (cnvlib.cnarray.CopyNumArray method)
U
unpipe_name() (in module cnvlib.importers)
W
warn_bad_probes() (in module cnvlib.reference)
write() (cnvlib.cnarray.CopyNumArray method)
write_tsv() (in module cnvlib.core)
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