hic3defdr
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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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K
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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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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() (hic3defdr.util.clusters.DirectedDisjointSet method)
add_columns_to_cluster_table() (in module hic3defdr.util.cluster_table)
align() (hic3defdr.util.banded_matrix.BandedMatrix class method)
AnalyzingHiC3DeFDR (class in hic3defdr.analysis.analysis)
apply() (hic3defdr.util.banded_matrix.BandedMatrix class method)
B
BandedMatrix (class in hic3defdr.util.banded_matrix)
bh() (hic3defdr.analysis.analysis.AnalyzingHiC3DeFDR method)
bias_patterns (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
bias_thresh (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
C
check_demo_data() (in module hic3defdr.util.demo_data)
chroms (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
classify() (hic3defdr.analysis.analysis.AnalyzingHiC3DeFDR method)
(in module hic3defdr.util.classification)
cluster_from_string() (in module hic3defdr.util.clusters)
cluster_to_loop_id() (in module hic3defdr.util.clusters)
cluster_to_slices() (in module hic3defdr.util.clusters)
clusters_to_coo() (in module hic3defdr.util.clusters)
clusters_to_pixel_set() (in module hic3defdr.util.clusters)
clusters_to_table() (in module hic3defdr.util.cluster_table)
cml() (in module hic3defdr.util.dispersion)
collect() (hic3defdr.analysis.analysis.AnalyzingHiC3DeFDR method)
compare_disp_fits() (in module hic3defdr.plotting.dispersion)
compute_fdr() (in module hic3defdr.util.evaluation)
conditional() (in module hic3defdr.util.scaling)
conditional_mor() (in module hic3defdr.util.scaling)
conditional_scaling() (in module hic3defdr.util.scaling)
context() (in module hic3defdr.util.progress)
convert_cluster_array_to_sparse() (in module hic3defdr.util.clusters)
copy() (hic3defdr.util.banded_matrix.BandedMatrix method)
CoreHiC3DeFDR (class in hic3defdr.analysis.core)
D
data_indices() (hic3defdr.util.banded_matrix.BandedMatrix method)
deconvolute() (hic3defdr.util.banded_matrix.BandedMatrix method)
(in module hic3defdr.util.matrices)
default() (hic3defdr.util.clusters.NumpyEncoder method)
design (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
dilate() (in module hic3defdr.util.matrices)
DirectedDisjointSet (class in hic3defdr.util.clusters)
E
ensure_demo_data() (in module hic3defdr.util.demo_data)
eprint() (in module hic3defdr.util.printing)
equal_bin() (in module hic3defdr.util.binning)
equalize() (in module hic3defdr.util.scaled_nb)
estimate_disp() (hic3defdr.analysis.alternatives.Global3DeFDR method)
(hic3defdr.analysis.alternatives.Poisson3DeFDR method)
(hic3defdr.analysis.alternatives.Unsmoothed3DeFDR method)
(hic3defdr.analysis.analysis.AnalyzingHiC3DeFDR method)
estimate_dispersion() (in module hic3defdr.util.dispersion)
evaluate() (hic3defdr.analysis.simulation.SimulatingHiC3DeFDR method)
(in module hic3defdr.util.evaluation)
F
filter_clusters_by_distance() (in module hic3defdr.util.clusters)
filter_sparse_rows_count() (in module hic3defdr.util.filtering)
find_clusters() (in module hic3defdr.util.clusters)
fit_mu_hat() (in module hic3defdr.util.scaled_nb)
flatten() (hic3defdr.util.banded_matrix.BandedMatrix method)
from_dia_matrix() (hic3defdr.util.banded_matrix.BandedMatrix class method)
from_ndarray() (hic3defdr.util.banded_matrix.BandedMatrix class method)
from_sparse() (hic3defdr.util.banded_matrix.BandedMatrix class method)
G
get_groups() (hic3defdr.util.clusters.DirectedDisjointSet method)
get_matrix() (hic3defdr.analysis.core.CoreHiC3DeFDR method)
Global3DeFDR (class in hic3defdr.analysis.alternatives)
H
HiC3DeFDR (class in hic3defdr.analysis.constructor)
hic3defdr (module)
hic3defdr.analysis (module)
hic3defdr.analysis.alternatives (module)
hic3defdr.analysis.analysis (module)
hic3defdr.analysis.constructor (module)
hic3defdr.analysis.core (module)
hic3defdr.analysis.plotting (module)
hic3defdr.analysis.simulation (module)
hic3defdr.plotting (module)
hic3defdr.plotting.dispersion (module)
hic3defdr.plotting.distance_bias (module)
hic3defdr.plotting.distance_dependence (module)
hic3defdr.plotting.fdr (module)
hic3defdr.plotting.fn_vs_fp (module)
hic3defdr.plotting.grid (module)
hic3defdr.plotting.heatmap (module)
hic3defdr.plotting.histograms (module)
hic3defdr.plotting.ma (module)
hic3defdr.plotting.roc (module)
hic3defdr.util (module)
hic3defdr.util.apa (module)
hic3defdr.util.balancing (module)
hic3defdr.util.banded_matrix (module)
hic3defdr.util.binning (module)
hic3defdr.util.classification (module)
hic3defdr.util.cluster_table (module)
hic3defdr.util.clusters (module)
hic3defdr.util.demo_data (module)
hic3defdr.util.dispersion (module)
hic3defdr.util.evaluation (module)
hic3defdr.util.filtering (module)
hic3defdr.util.lowess (module)
hic3defdr.util.lrt (module)
hic3defdr.util.matrices (module)
hic3defdr.util.parallelization (module)
hic3defdr.util.printing (module)
hic3defdr.util.progress (module)
hic3defdr.util.scaled_nb (module)
hic3defdr.util.scaling (module)
hic3defdr.util.simulation (module)
hic3defdr.util.thresholding (module)
hiccups_to_clusters() (in module hic3defdr.util.clusters)
I
inverse_mvr() (in module hic3defdr.util.scaled_nb)
is_bandedmatrix() (hic3defdr.util.banded_matrix.BandedMatrix class method)
is_upper() (hic3defdr.util.banded_matrix.BandedMatrix method)
K
kr_balance() (in module hic3defdr.util.balancing)
L
load() (hic3defdr.analysis.core.CoreHiC3DeFDR class method)
(hic3defdr.util.banded_matrix.BandedMatrix class method)
load_bias() (hic3defdr.analysis.core.CoreHiC3DeFDR method)
load_cluster_table() (in module hic3defdr.util.cluster_table)
load_clusters() (in module hic3defdr.util.clusters)
load_data() (hic3defdr.analysis.core.CoreHiC3DeFDR method)
load_disp_fn() (hic3defdr.analysis.core.CoreHiC3DeFDR method)
log() (hic3defdr.util.banded_matrix.BandedMatrix method)
logpmf() (in module hic3defdr.util.scaled_nb)
loop_patterns (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
lowess_fit() (in module hic3defdr.util.lowess)
lrt() (hic3defdr.analysis.alternatives.Poisson3DeFDR method)
(hic3defdr.analysis.analysis.AnalyzingHiC3DeFDR method)
(in module hic3defdr.util.lrt)
M
main() (in module hic3defdr.util.demo_data)
make_apa_stack() (in module hic3defdr.util.apa)
make_mask() (hic3defdr.util.banded_matrix.BandedMatrix static method)
make_upper() (hic3defdr.util.banded_matrix.BandedMatrix method)
make_y_true() (in module hic3defdr.util.evaluation)
max() (hic3defdr.util.banded_matrix.BandedMatrix class method)
max_range() (hic3defdr.util.banded_matrix.BandedMatrix method)
mean_thresh (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
median_of_ratios() (in module hic3defdr.util.scaling)
mme() (in module hic3defdr.util.dispersion)
mme_per_pixel() (in module hic3defdr.util.dispersion)
mvr() (in module hic3defdr.util.scaled_nb)
N
no_scaling() (in module hic3defdr.util.scaling)
NumpyEncoder (class in hic3defdr.util.clusters)
O
outdir (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
P
parallel_apply() (in module hic3defdr.util.parallelization)
parallel_map() (in module hic3defdr.util.parallelization)
perturb_cluster() (in module hic3defdr.util.simulation)
picklefile (hic3defdr.analysis.core.CoreHiC3DeFDR attribute)
plot_correlation_matrix() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
plot_dd_curves() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
(in module hic3defdr.plotting.distance_dependence)
plot_ddr() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
(in module hic3defdr.plotting.dispersion)
plot_dispersion_fit() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
plot_distance_bias() (in module hic3defdr.plotting.distance_bias)
plot_fdr() (in module hic3defdr.plotting.fdr)
plot_fn_vs_fp() (in module hic3defdr.plotting.fn_vs_fp)
plot_grid() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
(in module hic3defdr.plotting.grid)
plot_heatmap() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
(in module hic3defdr.plotting.heatmap)
plot_ma() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
(in module hic3defdr.plotting.ma)
plot_mvr() (in module hic3defdr.plotting.dispersion)
plot_pvalue_distribution() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
plot_pvalue_histogram() (in module hic3defdr.plotting.histograms)
plot_qvalue_distribution() (hic3defdr.analysis.plotting.PlottingHiC3DeFDR method)
plot_roc() (in module hic3defdr.plotting.roc)
PlottingHiC3DeFDR (class in hic3defdr.analysis.plotting)
Poisson3DeFDR (class in hic3defdr.analysis.alternatives)
poisson_fit_mu_hat() (in module hic3defdr.analysis.alternatives)
poisson_logpmf() (in module hic3defdr.analysis.alternatives)
poisson_lrt() (in module hic3defdr.analysis.alternatives)
prepare_data() (hic3defdr.analysis.analysis.AnalyzingHiC3DeFDR method)
Q
q2qnbinom() (in module hic3defdr.util.scaled_nb)
qcml() (in module hic3defdr.util.dispersion)
R
ravel() (hic3defdr.util.banded_matrix.BandedMatrix method)
raw_npz_patterns (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
res (hic3defdr.analysis.constructor.HiC3DeFDR attribute)
reshape() (hic3defdr.util.banded_matrix.BandedMatrix method)
roll_footprint() (in module hic3defdr.util.banded_matrix)
roll_matrix() (hic3defdr.util.banded_matrix.BandedMatrix static method)
run_to_qvalues() (hic3defdr.analysis.analysis.AnalyzingHiC3DeFDR method)
S
save() (hic3defdr.util.banded_matrix.BandedMatrix method)
save_clusters() (in module hic3defdr.util.clusters)
save_data() (hic3defdr.analysis.core.CoreHiC3DeFDR method)
save_disp_fn() (hic3defdr.analysis.core.CoreHiC3DeFDR method)
select_matrix() (in module hic3defdr.util.matrices)
simple_scaling() (in module hic3defdr.util.scaling)
simulate() (hic3defdr.analysis.simulation.SimulatingHiC3DeFDR method)
(in module hic3defdr.util.simulation)
SimulatingHiC3DeFDR (class in hic3defdr.analysis.simulation)
size_filter() (in module hic3defdr.util.thresholding)
sort_cluster_table() (in module hic3defdr.util.cluster_table)
sparse_intersection() (in module hic3defdr.util.matrices)
sparse_union() (in module hic3defdr.util.matrices)
symmetrize() (hic3defdr.util.banded_matrix.BandedMatrix method)
T
threshold() (hic3defdr.analysis.analysis.AnalyzingHiC3DeFDR method)
threshold_and_cluster() (in module hic3defdr.util.thresholding)
tqdm_maybe() (in module hic3defdr.util.progress)
U
Unsmoothed3DeFDR (class in hic3defdr.analysis.alternatives)
W
weighted_lowess_fit() (in module hic3defdr.util.lowess)
where() (hic3defdr.util.banded_matrix.BandedMatrix method)
wipe_distances() (in module hic3defdr.util.matrices)
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