cooltools
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Overview
Getting started
Tutorials
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Contacts vs distance
Compartments & Saddleplots
Insulation & boundaries
Dots & focal enrichment
Pileups and average features
Command line interface
Reference
CLI Reference
API Reference
Release notes
cooltools
Index
Edit on GitHub
Index
Symbols
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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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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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V
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W
|
Z
Symbols
--aggregate
cooltools-pileup command line option
--aggregate-smoothed
cooltools-expected-cis command line option
--all-names
cooltools-genome-binnify command line option
--append-raw-scores
cooltools-insulation command line option
--assembly
cooltools-rearrange command line option
--bigwig
cooltools-coverage command line option
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-insulation command line option
cooltools-virtual4c command line option
--chunksize
cooltools-coverage command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-insulation command line option
cooltools-random-sample command line option
cooltools-rearrange command line option
--cis-count
cooltools-random-sample command line option
--clr-weight-name
cooltools-dots command line option
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-insulation command line option
cooltools-pileup command line option
cooltools-saddle command line option
cooltools-virtual4c command line option
--clr_weight_name
cooltools-coverage command line option
--clustering-radius
cooltools-dots command line option
--cmap
cooltools-saddle command line option
--contact-type
cooltools-saddle command line option
--count
cooltools-random-sample command line option
--debug
cooltools command line option
--exact
cooltools-random-sample command line option
--expected
cooltools-pileup command line option
--fdr
cooltools-dots command line option
--features-format
cooltools-pileup command line option
--fig
cooltools-saddle command line option
--flank
cooltools-pileup command line option
--frac
cooltools-random-sample command line option
--hist-color
cooltools-saddle command line option
--ignore-diags
cooltools-coverage command line option
cooltools-eigs-cis command line option
cooltools-expected-cis command line option
cooltools-insulation command line option
cooltools-pileup command line option
--mapped-only
cooltools-genome-gc command line option
--max-dist
cooltools-saddle command line option
--max-loci-separation
cooltools-dots command line option
--max-nans-tolerated
cooltools-dots command line option
--min-dist
cooltools-saddle command line option
--min-dist-bad-bin
cooltools-insulation command line option
--min-frac-valid-pixels
cooltools-insulation command line option
--mode
cooltools-rearrange command line option
--n-bins
cooltools-saddle command line option
--n-eigs
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
--new-chrom-col
cooltools-rearrange command line option
--no-strength
cooltools-saddle command line option
--nproc
cooltools-coverage command line option
cooltools-dots command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-insulation command line option
cooltools-pileup command line option
cooltools-random-sample command line option
cooltools-virtual4c command line option
--num-lambda-bins
cooltools-dots command line option
--orientation-col
cooltools-rearrange command line option
--out
cooltools-pileup command line option
--out-format
cooltools-pileup command line option
--out-prefix
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-saddle command line option
cooltools-virtual4c command line option
--output
cooltools-coverage command line option
cooltools-dots command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-insulation command line option
--phasing-track
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
--qrange
cooltools-saddle command line option
--regions
cooltools-dots command line option
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-insulation command line option
cooltools-pileup command line option
cooltools-saddle command line option
--scale
cooltools-saddle command line option
--smooth
cooltools-expected-cis command line option
--smooth-sigma
cooltools-expected-cis command line option
--store
cooltools-coverage command line option
--store-snips
cooltools-pileup command line option
--strength
cooltools-saddle command line option
--threshold
cooltools-insulation command line option
--tile-size
cooltools-dots command line option
--verbose
cooltools command line option
cooltools-dots command line option
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-insulation command line option
cooltools-pileup command line option
cooltools-saddle command line option
--version
cooltools command line option
--view
cooltools-dots command line option
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-insulation command line option
cooltools-pileup command line option
cooltools-rearrange command line option
cooltools-saddle command line option
--vmax
cooltools-saddle command line option
--vmin
cooltools-saddle command line option
--vrange
cooltools-saddle command line option
--window-pixels
cooltools-insulation command line option
-c
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-random-sample command line option
-d
cooltools command line option
-f
cooltools-random-sample command line option
-n
cooltools-saddle command line option
-o
cooltools-coverage command line option
cooltools-dots command line option
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-insulation command line option
cooltools-pileup command line option
cooltools-saddle command line option
cooltools-virtual4c command line option
-p
cooltools-coverage command line option
cooltools-dots command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-insulation command line option
cooltools-pileup command line option
cooltools-random-sample command line option
cooltools-virtual4c command line option
-t
cooltools-saddle command line option
-V
cooltools command line option
-v
cooltools command line option
cooltools-dots command line option
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-pileup command line option
cooltools-saddle command line option
A
adaptive_coarsegrain() (in module cooltools.lib.numutils)
adjusted_exp_name() (in module cooltools.api.dotfinder)
align_track_with_cooler() (in module cooltools.lib.common)
annotate_pixels_with_qvalues() (in module cooltools.api.dotfinder)
assign_regions() (in module cooltools.lib.common)
assign_regions_to_bins() (in module cooltools.lib.common)
assign_supports() (in module cooltools.lib.common)
assign_view_auto() (in module cooltools.lib.common)
assign_view_paired() (in module cooltools.lib.common)
B
BINS_PATH
cooltools-genome-gc command line option
cooltools-genome-genecov command line option
BINSIZE
cooltools-genome-binnify command line option
blocksum_pairwise() (in module cooltools.api.expected)
bp_to_bins() (in module cooltools.api.dotfinder)
C
calculate_insulation_score() (in module cooltools.api.insulation)
CHROMSIZES_PATH
cooltools-genome-binnify command line option
cooltools-genome-digest command line option
cis_eig() (in module cooltools.api.eigdecomp)
clust_2D_pixels() (in module cooltools.api.dotfinder)
cluster_filtering_hiccups() (in module cooltools.api.dotfinder)
clustering_step() (in module cooltools.api.dotfinder)
coarsen() (in module cooltools.lib.numutils)
combine_binned_expected() (in module cooltools.api.expected)
COMED() (in module cooltools.lib.numutils)
COOL_PATH
cooltools-coverage command line option
cooltools-dots command line option
cooltools-eigs-cis command line option
cooltools-eigs-trans command line option
cooltools-expected-cis command line option
cooltools-expected-trans command line option
cooltools-pileup command line option
cooltools-saddle command line option
cooltools-virtual4c command line option
CoolerSnipper (class in cooltools.api.snipping)
cooltools command line option
--debug
--verbose
--version
-d
-v
-V
cooltools-coverage command line option
--bigwig
--chunksize
--clr_weight_name
--ignore-diags
--nproc
--output
--store
-o
-p
COOL_PATH
cooltools-dots command line option
--clr-weight-name
--clustering-radius
--fdr
--max-loci-separation
--max-nans-tolerated
--nproc
--num-lambda-bins
--output
--regions
--tile-size
--verbose
--view
-o
-p
-v
COOL_PATH
EXPECTED_PATH
cooltools-eigs-cis command line option
--bigwig
--clr-weight-name
--ignore-diags
--n-eigs
--out-prefix
--phasing-track
--regions
--verbose
--view
-o
-v
COOL_PATH
cooltools-eigs-trans command line option
--bigwig
--clr-weight-name
--n-eigs
--out-prefix
--phasing-track
--regions
--verbose
--view
-o
-v
COOL_PATH
cooltools-expected-cis command line option
--aggregate-smoothed
--chunksize
--clr-weight-name
--ignore-diags
--nproc
--output
--regions
--smooth
--smooth-sigma
--view
-c
-o
-p
COOL_PATH
cooltools-expected-trans command line option
--chunksize
--clr-weight-name
--nproc
--output
--regions
--view
-c
-o
-p
COOL_PATH
cooltools-genome-binnify command line option
--all-names
BINSIZE
CHROMSIZES_PATH
cooltools-genome-digest command line option
CHROMSIZES_PATH
ENZYME_NAME
FASTA_PATH
cooltools-genome-fetch-chromsizes command line option
DB
cooltools-genome-gc command line option
--mapped-only
BINS_PATH
FASTA_PATH
cooltools-genome-genecov command line option
BINS_PATH
DB
cooltools-insulation command line option
--append-raw-scores
--bigwig
--chunksize
--clr-weight-name
--ignore-diags
--min-dist-bad-bin
--min-frac-valid-pixels
--nproc
--output
--regions
--threshold
--verbose
--view
--window-pixels
-o
-p
IN_PATH
WINDOW
cooltools-pileup command line option
--aggregate
--clr-weight-name
--expected
--features-format
--flank
--ignore-diags
--nproc
--out
--out-format
--regions
--store-snips
--verbose
--view
-o
-p
-v
COOL_PATH
FEATURES_PATH
cooltools-random-sample command line option
--chunksize
--cis-count
--count
--exact
--frac
--nproc
-c
-f
-p
IN_PATH
OUT_PATH
cooltools-rearrange command line option
--assembly
--chunksize
--mode
--new-chrom-col
--orientation-col
--view
IN_PATH
OUT_PATH
cooltools-saddle command line option
--clr-weight-name
--cmap
--contact-type
--fig
--hist-color
--max-dist
--min-dist
--n-bins
--no-strength
--out-prefix
--qrange
--regions
--scale
--strength
--verbose
--view
--vmax
--vmin
--vrange
-n
-o
-t
-v
COOL_PATH
EXPECTED_PATH
TRACK_PATH
cooltools-virtual4c command line option
--bigwig
--clr-weight-name
--nproc
--out-prefix
-o
-p
COOL_PATH
VIEWPOINT
cooltools.api.coverage
module
cooltools.api.directionality
module
cooltools.api.dotfinder
module
cooltools.api.eigdecomp
module
cooltools.api.expected
module
cooltools.api.insulation
module
cooltools.api.saddle
module
cooltools.api.sample
module
cooltools.api.snipping
module
cooltools.api.virtual4c
module
cooltools.lib.common
module
cooltools.lib.numutils
module
cooltools.lib.peaks
module
cooltools.lib.plotting
module
cooltools.lib.schemas
module
count_all_pixels_per_block() (in module cooltools.api.expected)
count_all_pixels_per_diag() (in module cooltools.api.expected)
count_bad_pixels_per_block() (in module cooltools.api.expected)
count_bad_pixels_per_diag() (in module cooltools.api.expected)
coverage() (in module cooltools.api.coverage)
D
DB
cooltools-genome-fetch-chromsizes command line option
cooltools-genome-genecov command line option
determine_thresholds() (in module cooltools.api.dotfinder)
diagsum_from_array() (in module cooltools.api.expected)
diagsum_pairwise() (in module cooltools.api.expected)
diagsum_symm() (in module cooltools.api.expected)
digitize() (in module cooltools.api.saddle)
directionality() (in module cooltools.api.directionality)
dist_to_mask() (in module cooltools.lib.numutils)
dots() (in module cooltools.api.dotfinder)
E
eigs_cis() (in module cooltools.api.eigdecomp)
eigs_trans() (in module cooltools.api.eigdecomp)
ENZYME_NAME
cooltools-genome-digest command line option
expand_align_features() (in module cooltools.api.snipping)
expected_cis() (in module cooltools.api.expected)
EXPECTED_PATH
cooltools-dots command line option
cooltools-saddle command line option
expected_trans() (in module cooltools.api.expected)
ExpectedSnipper (class in cooltools.api.snipping)
extract_scored_pixels() (in module cooltools.api.dotfinder)
F
FASTA_PATH
cooltools-genome-digest command line option
cooltools-genome-gc command line option
FEATURES_PATH
cooltools-pileup command line option
fill_diag() (in module cooltools.lib.numutils)
fill_inf() (in module cooltools.lib.numutils)
fill_na() (in module cooltools.lib.numutils)
fill_nainf() (in module cooltools.lib.numutils)
find_boundaries() (in module cooltools.api.insulation)
find_peak_prominence() (in module cooltools.lib.peaks)
find_peak_prominence_iterative() (in module cooltools.lib.peaks)
G
generate_tiles_diag_band() (in module cooltools.api.dotfinder)
genomewide_smooth_cvd() (in module cooltools.api.expected)
get_adjusted_expected_tile_some_nans() (in module cooltools.api.dotfinder)
get_cmap() (in module cooltools.lib.plotting)
get_diag() (in module cooltools.lib.numutils)
get_eig() (in module cooltools.lib.numutils)
get_finite() (in module cooltools.lib.numutils)
get_kernel() (in module cooltools.lib.numutils)
get_n_pixels() (in module cooltools.api.insulation)
gridspec_inches() (in module cooltools.lib.plotting)
H
histogram_scored_pixels() (in module cooltools.api.dotfinder)
I
IN_PATH
cooltools-insulation command line option
cooltools-random-sample command line option
cooltools-rearrange command line option
infer_mask2D() (in module cooltools.lib.numutils)
insul_diamond() (in module cooltools.api.insulation)
insulation() (in module cooltools.api.insulation)
interp_nan() (in module cooltools.lib.numutils)
interpolate_bad_singletons() (in module cooltools.lib.numutils)
interpolate_expected() (in module cooltools.api.expected)
is_compatible_kernels() (in module cooltools.api.dotfinder)
is_symmetric() (in module cooltools.lib.numutils)
L
lattice_pdist_frequencies() (in module cooltools.api.expected)
list_to_colormap() (in module cooltools.lib.plotting)
logbin_expected() (in module cooltools.api.expected)
M
MAD() (in module cooltools.lib.numutils)
make_bin_aligned_windows() (in module cooltools.api.snipping)
make_block_table() (in module cooltools.api.expected)
make_cooler_view() (in module cooltools.lib.common)
make_diag_table() (in module cooltools.api.expected)
make_diag_tables() (in module cooltools.api.expected)
mask_cooler_bad_bins() (in module cooltools.lib.common)
module
cooltools.api.coverage
cooltools.api.directionality
cooltools.api.dotfinder
cooltools.api.eigdecomp
cooltools.api.expected
cooltools.api.insulation
cooltools.api.saddle
cooltools.api.sample
cooltools.api.snipping
cooltools.api.virtual4c
cooltools.lib.common
cooltools.lib.numutils
cooltools.lib.peaks
cooltools.lib.plotting
cooltools.lib.schemas
N
nans_inkernel_name() (in module cooltools.api.dotfinder)
normalize_score() (in module cooltools.lib.numutils)
O
ObsExpSnipper (class in cooltools.api.snipping)
OUT_PATH
cooltools-random-sample command line option
cooltools-rearrange command line option
P
peakdet() (in module cooltools.lib.peaks)
per_region_smooth_cvd() (in module cooltools.api.expected)
persistent_log_bins() (in module cooltools.lib.numutils)
pileup() (in module cooltools.api.snipping)
pool_decorator() (in module cooltools.lib.common)
R
recommend_kernels() (in module cooltools.api.dotfinder)
remove_good_singletons() (in module cooltools.lib.numutils)
robust_gauss_filter() (in module cooltools.lib.numutils)
S
saddle() (in module cooltools.api.saddle)
saddle_strength() (in module cooltools.api.saddle)
saddleplot() (in module cooltools.api.saddle)
sample() (in module cooltools.api.sample)
sample_pixels_approx() (in module cooltools.api.sample)
sample_pixels_exact() (in module cooltools.api.sample)
score_tile() (in module cooltools.api.dotfinder)
scoring_and_extraction_step() (in module cooltools.api.dotfinder)
scoring_and_histogramming_step() (in module cooltools.api.dotfinder)
select() (cooltools.api.snipping.CoolerSnipper method)
(cooltools.api.snipping.ExpectedSnipper method)
(cooltools.api.snipping.ObsExpSnipper method)
set_diag() (in module cooltools.lib.numutils)
slice_sorted() (in module cooltools.lib.numutils)
smooth() (in module cooltools.lib.numutils)
snip() (cooltools.api.snipping.CoolerSnipper method)
(cooltools.api.snipping.ExpectedSnipper method)
(cooltools.api.snipping.ObsExpSnipper method)
stochastic_sd() (in module cooltools.lib.numutils)
T
tile_square_matrix() (in module cooltools.api.dotfinder)
TRACK_PATH
cooltools-saddle command line option
trans_eig() (in module cooltools.api.eigdecomp)
V
view_from_track() (in module cooltools.lib.common)
VIEWPOINT
cooltools-virtual4c command line option
virtual4c() (in module cooltools.api.virtual4c)
W
weighted_groupby_mean() (in module cooltools.lib.numutils)
WINDOW
cooltools-insulation command line option
Z
zoom_array() (in module cooltools.lib.numutils)
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