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lib5c
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A
abs_diff_counts() (in module lib5c.util.counts)
add_ax() (lib5c.plotters.extendable.extendable_figure.ExtendableFigure method)
add_bed_track() (lib5c.plotters.extendable.bed_extendable_heatmap.BedExtendableHeatmap method)
add_bed_tracks() (lib5c.plotters.extendable.bed_extendable_heatmap.BedExtendableHeatmap method)
add_bias_heatmap_tool() (in module lib5c.tools.bias_heatmap)
add_bin_tool() (in module lib5c.tools.bin)
add_boxplot_tool() (in module lib5c.tools.boxplot)
add_chipseq_track() (lib5c.plotters.extendable.chipseq_extendable_heatmap.ChipSeqExtendableHeatmap method)
add_chipseq_tracks() (lib5c.plotters.extendable.chipseq_extendable_heatmap.ChipSeqExtendableHeatmap method)
add_clusters() (lib5c.plotters.extendable.cluster_extendable_heatmap.ClusterExtendableHeatmap method)
add_colorbar() (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap method)
(lib5c.plotters.extendable.extendable_figure.ExtendableFigure method)
add_colorscale_tool() (in module lib5c.tools.colorscale)
add_column_from_counts() (lib5c.structures.dataset.Dataset method)
add_columns_from_counts_superdict() (lib5c.structures.dataset.Dataset method)
add_convergency_tool() (in module lib5c.tools.convergency)
add_correlation_tool() (in module lib5c.tools.correlation)
add_dd_curve_tool() (in module lib5c.tools.dd_curve)
add_determine_bins_tool() (in module lib5c.tools.determine_bins)
add_distribution_tool() (in module lib5c.tools.distribution)
add_divide_tool() (in module lib5c.tools.divide)
add_enrichment_tool() (in module lib5c.tools.enrichment)
add_expected_tool() (in module lib5c.tools.expected)
add_express_tool() (in module lib5c.tools.express)
add_gene_stack() (lib5c.plotters.extendable.gene_extendable_heatmap.GeneExtendableHeatmap method)
add_gene_stacks() (lib5c.plotters.extendable.gene_extendable_heatmap.GeneExtendableHeatmap method)
add_gene_track() (lib5c.plotters.extendable.gene_extendable_heatmap.GeneExtendableHeatmap method)
add_gene_tracks() (lib5c.plotters.extendable.gene_extendable_heatmap.GeneExtendableHeatmap method)
add_heatmap_tool() (in module lib5c.tools.heatmap)
add_hic_extract_tool() (in module lib5c.tools.hic_extract)
add_iced_tool() (in module lib5c.tools.iced)
add_interaction_score_tool() (in module lib5c.tools.interaction_score)
add_kr_tool() (in module lib5c.tools.kr)
add_legend() (lib5c.plotters.extendable.legend_extendable_heatmap.LegendExtendableHeatmap method)
add_log_tool() (in module lib5c.tools.log)
add_margin_ax() (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap method)
add_motif_track() (lib5c.plotters.extendable.motif_extendable_heatmap.MotifExtendableHeatmap method)
add_motif_tracks() (lib5c.plotters.extendable.motif_extendable_heatmap.MotifExtendableHeatmap method)
add_outliers_tool() (in module lib5c.tools.outliers)
add_pca_tool() (in module lib5c.tools.pca)
add_pipeline_tool() (in module lib5c.tools.pipeline)
add_pvalue_histogram_tool() (in module lib5c.tools.pvalue_histogram)
add_pvalues_tool() (in module lib5c.tools.pvalues)
add_qnorm_tool() (in module lib5c.tools.qnorm)
add_qvalues_tool() (in module lib5c.tools.qvalues)
add_rectangle() (lib5c.plotters.extendable.rectangle_extendable_heatmap.RectangleExtendableHeatmap method)
add_rectangles() (lib5c.plotters.extendable.rectangle_extendable_heatmap.RectangleExtendableHeatmap method)
add_refgene_stack() (lib5c.plotters.extendable.gene_extendable_heatmap.GeneExtendableHeatmap method)
add_refgene_stacks() (lib5c.plotters.extendable.gene_extendable_heatmap.GeneExtendableHeatmap method)
add_remove_tool() (in module lib5c.tools.remove)
add_ruler() (lib5c.plotters.extendable.ruler_extendable_heatmap.RulerExtendableHeatmap method)
add_rulers() (lib5c.plotters.extendable.ruler_extendable_heatmap.RulerExtendableHeatmap method)
add_smooth_tool() (in module lib5c.tools.smooth)
add_snp_track() (lib5c.plotters.extendable.snp_extendable_heatmap.SNPExtendableHeatmap method)
add_snp_tracks() (lib5c.plotters.extendable.snp_extendable_heatmap.SNPExtendableHeatmap method)
add_spline_tool() (in module lib5c.tools.spline)
add_subtract_tool() (in module lib5c.tools.subtract)
add_threshold_tool() (in module lib5c.tools.threshold)
add_trim_tool() (in module lib5c.tools.trim)
add_variance_tool() (in module lib5c.tools.variance)
add_visualization_hooks() (in module lib5c.contrib.luigi.tasks)
add_visualize_fits_tool() (in module lib5c.tools.visualize_fits)
add_visualize_splines_tool() (in module lib5c.tools.visualize_splines)
add_visualize_variance_tool() (in module lib5c.tools.visualize_variance)
adjust_plot() (in module lib5c.util.plotting)
adjust_pvalues() (in module lib5c.util.statistics)
agg_fn (lib5c.contrib.luigi.tasks.VarianceTask attribute)
aggregate_primermap() (in module lib5c.util.primers)
all_reps (lib5c.contrib.luigi.pipeline.TreeMixin attribute)
amean_gaussian() (in module lib5c.algorithms.filtering.filter_functions)
amean_inverse() (in module lib5c.algorithms.filtering.filter_functions)
Annotatable (class in lib5c.core.mixins)
apply() (lib5c.operators.base.InteractionMatrixOperator method)
(lib5c.operators.base.MultiInteractionMatrixOperator method)
apply_across_replicates() (lib5c.structures.dataset.Dataset method)
apply_across_replicates_per_region() (lib5c.structures.dataset.Dataset method)
apply_by_region() (lib5c.operators.base.InteractionMatrixOperator method)
(lib5c.operators.base.MultiInteractionMatrixOperator method)
apply_filter() (in module lib5c.algorithms.donut_filters)
apply_inplace() (lib5c.operators.base.InteractionMatrixOperator method)
(lib5c.operators.base.MultiInteractionMatrixOperator method)
(lib5c.operators.modeling.EmpiricalPvalueOperator method)
(lib5c.operators.qnorm.QuantileNormalizer method)
(lib5c.operators.standardization.Standardizer method)
(lib5c.operators.trimming.InteractionTrimmer method)
(lib5c.operators.trimming.LocusTrimmer method)
apply_nonredundant() (in module lib5c.util.counts)
apply_nonredundant_parallel() (in module lib5c.util.counts)
apply_per_region() (lib5c.structures.dataset.Dataset method)
apply_per_replicate() (lib5c.structures.dataset.Dataset method)
apply_per_replicate_per_region() (lib5c.structures.dataset.Dataset method)
arithmetic_mean() (in module lib5c.algorithms.filtering.filter_functions)
array (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap attribute)
array_index_to_peaks() (in module lib5c.algorithms.clustering.util)
array_newton() (in module lib5c.util.optimization)
as_dict() (lib5c.core.loci.Locus method)
as_dict_of_list_of_dict() (lib5c.core.loci.LocusMap method)
as_list_of_dict() (lib5c.core.loci.LocusMap method)
averaging (lib5c.contrib.luigi.pipeline.MakeQnorm attribute)
(lib5c.contrib.luigi.tasks.QnormTask attribute)
axes (lib5c.plotters.extendable.extendable_figure.ExtendableFigure attribute)
B
background_threshold (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
balance_matrix() (in module lib5c.algorithms.knight_ruiz)
BaseExtendableHeatmap (class in lib5c.plotters.extendable.base_extendable_heatmap)
BedExtendableHeatmap (class in lib5c.plotters.extendable.bed_extendable_heatmap)
belongs_to() (in module lib5c.algorithms.clustering.util)
belongs_to_which() (in module lib5c.algorithms.clustering.util)
bh_fdr (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
bias (lib5c.contrib.luigi.tasks.ExpressTask attribute)
(lib5c.contrib.luigi.tasks.IcedTask attribute)
(lib5c.contrib.luigi.tasks.KnightRuizTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesOneTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
bias_factors (lib5c.contrib.luigi.tasks.SplineTask attribute)
bias_heatmap_tool() (in module lib5c.tools.bias_heatmap)
BigWig (class in lib5c.contrib.pybigwig.bigwig)
bigwig_avail() (in module lib5c.contrib.pybigwig.bigwig)
bin_bin_filter() (in module lib5c.algorithms.filtering.bin_bin_filtering)
bin_bin_filter_counts() (in module lib5c.algorithms.filtering.bin_bin_filtering)
bin_tool() (in module lib5c.tools.bin)
bin_width (lib5c.contrib.luigi.pipeline.MakeBinned attribute)
(lib5c.contrib.luigi.tasks.DetermineBinsTask attribute)
BinTask (class in lib5c.contrib.luigi.tasks)
boxplot_tool() (in module lib5c.tools.boxplot)
bw (lib5c.contrib.pybigwig.bigwig.BigWig attribute)
by_index() (lib5c.core.loci.LocusMap method)
by_name() (lib5c.core.loci.LocusMap method)
by_region_index() (lib5c.core.loci.LocusMap method)
C
calculate_pvalues() (in module lib5c.util.counts)
calculate_regional_pvalues() (in module lib5c.util.counts)
call_pvalues() (in module lib5c.util.distributions)
center_of_mass() (in module lib5c.algorithms.clustering.util)
check_intersect() (in module lib5c.util.bed)
check_neighboorhood_nonnan() (in module lib5c.algorithms.filtering.filter_functions)
check_neighboorhood_positive() (in module lib5c.algorithms.filtering.filter_functions)
check_outdir() (in module lib5c.util.system)
ChipSeqExtendableHeatmap (class in lib5c.plotters.extendable.chipseq_extendable_heatmap)
chrom (lib5c.core.loci.Locus attribute)
classify_peak() (in module lib5c.algorithms.clustering.knn)
clear_enrichment_caches() (in module lib5c.algorithms.enrichment)
close() (lib5c.plotters.extendable.extendable_figure.ExtendableFigure method)
ClusterExtendableHeatmap (class in lib5c.plotters.extendable.cluster_extendable_heatmap)
clusters_to_array() (in module lib5c.algorithms.clustering.util)
CmdTask (class in lib5c.contrib.luigi.tasks)
cohens_kappa() (in module lib5c.util.metrics)
color_confusion() (in module lib5c.algorithms.thresholding)
colormap (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap attribute)
colorscale (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap attribute)
colorscale_tool() (in module lib5c.tools.colorscale)
compute_bounding_box() (in module lib5c.plotters.clustering)
compute_convergency() (in module lib5c.algorithms.convergency)
compute_hexbin_extent() (in module lib5c.util.plotting)
compute_pca() (in module lib5c.algorithms.pca)
compute_pca_from_counts_superdict() (in module lib5c.algorithms.pca)
compute_regional_obs_over_exp_scale() (in module lib5c.util.scales)
compute_regional_obs_scale() (in module lib5c.util.scales)
compute_track_scales() (in module lib5c.util.scales)
concordance_confusion() (in module lib5c.algorithms.thresholding)
concordant (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
condition_on (lib5c.contrib.luigi.pipeline.MakeQnorm attribute)
(lib5c.contrib.luigi.tasks.QnormTask attribute)
conditions (lib5c.contrib.luigi.tasks.CrossVarianceTask attribute)
(lib5c.contrib.luigi.tasks.ThresholdTask attribute)
conservative_qcut() (in module lib5c.util.stratification)
constant_fit() (in module lib5c.util.lowess)
convergency_tool() (in module lib5c.tools.convergency)
convert_grange_to_slice() (in module lib5c.util.slicing)
convert_parameters() (in module lib5c.util.distributions)
convert_pvalues_to_interaction_scores() (in module lib5c.util.counts)
convert_slice_to_grange() (in module lib5c.util.slicing)
convert_to_two_tail() (in module lib5c.util.statistics)
correlation_tool() (in module lib5c.tools.correlation)
count_clusters() (in module lib5c.algorithms.thresholding)
count_intersections() (in module lib5c.algorithms.enrichment)
(in module lib5c.util.bed)
count_intersections_all() (in module lib5c.algorithms.enrichment)
counts() (lib5c.structures.dataset.Dataset method)
counts_superdict_to_matrix() (in module lib5c.util.counts_superdict)
countsfiles (lib5c.contrib.luigi.pipeline.RawCounts attribute)
cross_rep_plus_deviation_variance() (in module lib5c.algorithms.variance.combined)
cross_rep_variance() (in module lib5c.algorithms.variance.cross_rep)
CrossVarianceTask (class in lib5c.contrib.luigi.tasks)
CustomHelpFormatter (class in lib5c.tools.lib5c_toolbox)
D
data (lib5c.core.loci.Locus attribute)
(lib5c.core.mixins.Annotatable attribute)
Dataset (class in lib5c.structures.dataset)
dataset_outfile (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
dblalt_primer_parser() (in module lib5c.parsers.primer_names)
dd_curve_tool() (in module lib5c.tools.dd_curve)
default_bin_namer() (in module lib5c.algorithms.determine_bins)
default_bin_parser() (in module lib5c.parsers.primer_names)
default_primer_parser() (in module lib5c.parsers.primer_names)
degree (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
delete() (lib5c.core.interactions.InteractionMatrix method)
(lib5c.core.loci.LocusMap method)
determine_bins_tool() (in module lib5c.tools.determine_bins)
determine_region_order() (in module lib5c.util.primers)
determine_regional_bins() (in module lib5c.algorithms.determine_bins)
DetermineBins (class in lib5c.contrib.luigi.pipeline)
DetermineBinsTask (class in lib5c.contrib.luigi.tasks)
deviation_variance() (in module lib5c.algorithms.variance.deviation)
df (lib5c.structures.dataset.Dataset attribute)
direction_score() (in module lib5c.algorithms.clustering.knn)
directory (lib5c.contrib.luigi.pipeline.TreeMixin attribute)
directory_to_task() (in module lib5c.contrib.luigi.pipeline)
DiscreteBivariateEmpiricalSurface (class in lib5c.algorithms.spline_normalization)
dispersion_to_variance() (in module lib5c.algorithms.variance.lognorm_dispersion)
(in module lib5c.algorithms.variance.nbinom_dispersion)
dispersion_to_variance_direct() (in module lib5c.algorithms.variance.lognorm_dispersion)
dist (lib5c.contrib.luigi.tasks.DistributionTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
distance_filter() (in module lib5c.util.counts)
distance_scale (lib5c.contrib.luigi.tasks.LegacyVisualizeFitTask attribute)
distance_score() (in module lib5c.algorithms.clustering.knn)
distance_threshold (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
distance_tolerance (lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
distribtion_tool() (in module lib5c.tools.distribution)
distribution (lib5c.contrib.luigi.tasks.PvalueTask attribute)
DistributionTask (class in lib5c.contrib.luigi.tasks)
divide_regional_counts() (in module lib5c.util.counts)
divide_tool() (in module lib5c.tools.divide)
divider (lib5c.plotters.extendable.extendable_figure.ExtendableFigure attribute)
DivideTask (class in lib5c.contrib.luigi.tasks)
DomainExtendableHeatmap (class in lib5c.plotters.extendable.domain_extendable_heatmap)
donut (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
donut_filt() (in module lib5c.algorithms.donut_filters)
donut_footprint() (in module lib5c.util.donut)
donut_frac (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
download_gzipped_file() (in module lib5c.util.demo_data)
drop_config_file() (in module lib5c.contrib.luigi.config)
dropna() (lib5c.structures.dataset.Dataset method)
E
edit_demo_config() (in module lib5c.util.demo_data)
empirical_binned() (in module lib5c.algorithms.expected)
EmpiricalPvalueOperator (class in lib5c.operators.modeling)
end (lib5c.core.loci.Locus attribute)
enrichment_tool() (in module lib5c.tools.enrichment)
ensure_demo_data() (in module lib5c.util.demo_data)
estimate_variance() (in module lib5c.algorithms.variance.estimate_variance)
ev() (lib5c.algorithms.spline_normalization.DiscreteBivariateEmpiricalSurface method)
eval_() (in module lib5c.util.ast_eval)
eval_expr() (in module lib5c.util.ast_eval)
exclude_near_diagonal (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
expected_tool() (in module lib5c.tools.expected)
expected_value (lib5c.contrib.luigi.tasks.LegacyVisualizeFitTask attribute)
ExpectedTask (class in lib5c.contrib.luigi.tasks)
express_normalize_matrix() (in module lib5c.algorithms.express)
express_tool() (in module lib5c.tools.express)
ExpressTask (class in lib5c.contrib.luigi.tasks)
ExtendableFigure (class in lib5c.plotters.extendable.extendable_figure)
ExtendableHeatmap (class in lib5c.plotters.extendable.extendable_heatmap)
extract_queried_counts() (in module lib5c.util.counts)
extract_region() (lib5c.core.interactions.InteractionMatrix method)
(lib5c.core.loci.LocusMap method)
extract_slice() (lib5c.core.interactions.InteractionMatrix method)
(lib5c.core.loci.LocusMap method)
F
features_to_interlaps() (in module lib5c.contrib.interlap.util)
fig (lib5c.plotters.extendable.extendable_figure.ExtendableFigure attribute)
filter_near_diagonal() (in module lib5c.algorithms.thresholding)
filter_selector() (in module lib5c.algorithms.filtering.util)
FilteringTask (class in lib5c.contrib.luigi.tasks)
find_nearby_bins() (in module lib5c.algorithms.filtering.bin_bin_filtering)
find_nearby_fragments() (in module lib5c.algorithms.filtering.fragment_bin_filtering)
(in module lib5c.algorithms.filtering.fragment_fragment_filtering)
find_prebinned_unsmoothable_columns() (in module lib5c.algorithms.filtering.unsmoothable_columns)
find_unsmoothable_columns() (in module lib5c.algorithms.filtering.unsmoothable_columns)
find_upstream_primers() (in module lib5c.algorithms.filtering.fragment_bin_filtering)
fit_spline() (in module lib5c.algorithms.spline_normalization)
fitter (lib5c.contrib.luigi.tasks.VarianceTask attribute)
flag_array_high_spatial_outliers() (in module lib5c.algorithms.outliers)
flatten() (lib5c.core.interactions.InteractionMatrix method)
flatten_and_filter_counts() (in module lib5c.util.counts)
flatten_cis() (lib5c.core.interactions.InteractionMatrix method)
flatten_clusters() (in module lib5c.algorithms.clustering.util)
flatten_counts() (in module lib5c.util.counts)
flatten_counts_to_list() (in module lib5c.util.counts)
flatten_features() (in module lib5c.util.bed)
flatten_obs_and_exp() (in module lib5c.util.counts)
flatten_obs_and_exp_counts() (in module lib5c.util.counts)
flatten_regional_counts() (in module lib5c.util.counts)
flip_pvalues() (in module lib5c.util.counts)
fold_pvalues() (in module lib5c.util.counts)
fold_threshold (lib5c.contrib.luigi.tasks.OutliersTask attribute)
fold_threshold_lower (lib5c.operators.trimming.LocusTrimmer attribute)
fold_threshold_upper (lib5c.operators.trimming.LocusTrimmer attribute)
force_monotonic() (in module lib5c.algorithms.expected)
format_help() (lib5c.tools.lib5c_toolbox.CustomHelpFormatter method)
fractional_tolerance (lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
fragment_bin_filter() (in module lib5c.algorithms.filtering.fragment_bin_filtering)
fragment_bin_filter_counts() (in module lib5c.algorithms.filtering.fragment_bin_filtering)
fragment_fragment_filter() (in module lib5c.algorithms.filtering.fragment_fragment_filtering)
fragment_fragment_filter_counts() (in module lib5c.algorithms.filtering.fragment_fragment_filtering)
freeze_distribution() (in module lib5c.util.distributions)
from_binfile() (lib5c.core.interactions.InteractionMatrix class method)
(lib5c.core.loci.LocusMap class method)
from_counts_superdict() (lib5c.structures.dataset.Dataset class method)
from_countsfile() (lib5c.core.interactions.InteractionMatrix class method)
from_list() (lib5c.core.interactions.InteractionMatrix class method)
(lib5c.core.loci.LocusMap class method)
from_list_of_dict() (lib5c.core.loci.LocusMap class method)
from_locusmap() (lib5c.core.interactions.InteractionMatrix class method)
from_pickle() (lib5c.core.mixins.Picklable class method)
from_primerfile() (lib5c.core.interactions.InteractionMatrix class method)
(lib5c.core.loci.LocusMap class method)
from_size() (lib5c.core.interactions.InteractionMatrix class method)
from_table_file() (lib5c.structures.dataset.Dataset class method)
G
GeneExtendableHeatmap (class in lib5c.plotters.extendable.gene_extendable_heatmap)
geometric_mean() (in module lib5c.algorithms.filtering.filter_functions)
get_all_lines() (in module lib5c.contrib.luigi.tasks)
get_annotation_percentage() (in module lib5c.algorithms.enrichment)
get_annotation_percentage_all() (in module lib5c.algorithms.enrichment)
get_cluster() (in module lib5c.algorithms.clustering.util)
get_colormap() (in module lib5c.plotters.colormaps)
get_data() (lib5c.core.mixins.Annotatable method)
get_distance_expected() (in module lib5c.algorithms.expected)
get_fisher_exact_pvalue() (in module lib5c.algorithms.enrichment)
get_fisher_exact_pvalue_all() (in module lib5c.algorithms.enrichment)
get_fold_change() (in module lib5c.algorithms.enrichment)
get_fold_change_all() (in module lib5c.algorithms.enrichment)
get_global_distance_expected() (in module lib5c.algorithms.expected)
get_index() (lib5c.core.loci.LocusMap method)
get_index_by_hash() (lib5c.core.loci.LocusMap method)
get_inner_task_class() (lib5c.contrib.luigi.pipeline.JointTask method)
(lib5c.contrib.luigi.pipeline.MakeJointExpress method)
(lib5c.contrib.luigi.pipeline.MakeQnorm method)
get_inner_task_param_dict() (lib5c.contrib.luigi.pipeline.JointTask method)
get_inner_task_params() (lib5c.contrib.luigi.pipeline.JointTask method)
(lib5c.contrib.luigi.pipeline.MakeQnorm method)
get_knn() (in module lib5c.algorithms.clustering.knn)
get_log() (lib5c.core.mixins.Loggable method)
get_mid_to_mid_distance() (in module lib5c.util.bed)
get_midpoint() (in module lib5c.util.bed)
get_name() (lib5c.core.loci.Locus method)
get_pixelmap_legacy() (in module lib5c.parsers.primers)
get_region() (lib5c.core.loci.Locus method)
get_region_sizes() (lib5c.core.loci.LocusMap method)
get_regions() (lib5c.core.interactions.InteractionMatrix method)
(lib5c.core.loci.LocusMap method)
get_rep_index() (lib5c.contrib.luigi.pipeline.JointTask method)
get_strand() (lib5c.core.loci.Locus method)
get_value() (lib5c.core.mixins.Annotatable method)
get_vector() (in module lib5c.algorithms.clustering.util)
global_empirical_binned() (in module lib5c.algorithms.expected)
global_expected (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
global_fold_threshold_lower (lib5c.operators.trimming.InteractionTrimmer attribute)
global_fold_threshold_upper (lib5c.operators.trimming.InteractionTrimmer attribute)
global_lowess_binned() (in module lib5c.algorithms.expected)
global_lowess_binned_log_counts() (in module lib5c.algorithms.expected)
global_lowess_log_log_binned() (in module lib5c.algorithms.expected)
global_lowess_log_log_fragment() (in module lib5c.algorithms.expected)
global_percentage_threshold_lower (lib5c.operators.trimming.InteractionTrimmer attribute)
global_percentage_threshold_upper (lib5c.operators.trimming.InteractionTrimmer attribute)
global_poly_log_log_binned() (in module lib5c.algorithms.expected)
global_poly_log_log_fragment() (in module lib5c.algorithms.expected)
global_powerlaw_binned() (in module lib5c.algorithms.expected)
gmean() (in module lib5c.util.mathematics)
gmean_gaussian() (in module lib5c.algorithms.filtering.filter_functions)
gmean_inverse() (in module lib5c.algorithms.filtering.filter_functions)
grange_x (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap attribute)
grange_y (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap attribute)
group_fit() (in module lib5c.util.lowess)
group_obs_by_exp() (in module lib5c.util.grouping)
grouping (lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
guess_bin_step() (in module lib5c.util.primers)
guess_primer_name_parser() (in module lib5c.parsers.primer_names)
H
hash_to_index_dict (lib5c.core.loci.LocusMap attribute)
heatmap (lib5c.contrib.luigi.pipeline.MakeJointExpress attribute)
(lib5c.contrib.luigi.pipeline.MakeQnorm attribute)
(lib5c.contrib.luigi.pipeline.MakeRaw attribute)
(lib5c.contrib.luigi.tasks.BinTask attribute)
(lib5c.contrib.luigi.tasks.DivideTask attribute)
(lib5c.contrib.luigi.tasks.ExpectedTask attribute)
(lib5c.contrib.luigi.tasks.ExpressTask attribute)
(lib5c.contrib.luigi.tasks.IcedTask attribute)
(lib5c.contrib.luigi.tasks.InteractionScoreTask attribute)
(lib5c.contrib.luigi.tasks.KnightRuizTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesOneTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
(lib5c.contrib.luigi.tasks.OutliersTask attribute)
(lib5c.contrib.luigi.tasks.PvalueTask attribute)
(lib5c.contrib.luigi.tasks.QnormTask attribute)
(lib5c.contrib.luigi.tasks.QvaluesTask attribute)
(lib5c.contrib.luigi.tasks.SmoothTask attribute)
(lib5c.contrib.luigi.tasks.SplineTask attribute)
(lib5c.contrib.luigi.tasks.SubtractTask attribute)
(lib5c.contrib.luigi.tasks.ThresholdTask attribute)
heatmap_outdir (lib5c.contrib.luigi.pipeline.MakeJointExpress attribute)
(lib5c.contrib.luigi.pipeline.MakeQnorm attribute)
(lib5c.contrib.luigi.pipeline.MakeRaw attribute)
(lib5c.contrib.luigi.tasks.BinTask attribute)
(lib5c.contrib.luigi.tasks.DivideTask attribute)
(lib5c.contrib.luigi.tasks.ExpectedTask attribute)
(lib5c.contrib.luigi.tasks.ExpressTask attribute)
(lib5c.contrib.luigi.tasks.IcedTask attribute)
(lib5c.contrib.luigi.tasks.InteractionScoreTask attribute)
(lib5c.contrib.luigi.tasks.KnightRuizTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesOneTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
(lib5c.contrib.luigi.tasks.OutliersTask attribute)
(lib5c.contrib.luigi.tasks.PvalueTask attribute)
(lib5c.contrib.luigi.tasks.QnormTask attribute)
(lib5c.contrib.luigi.tasks.QvaluesTask attribute)
(lib5c.contrib.luigi.tasks.SmoothTask attribute)
(lib5c.contrib.luigi.tasks.SplineTask attribute)
(lib5c.contrib.luigi.tasks.SubtractTask attribute)
(lib5c.contrib.luigi.tasks.ThresholdTask attribute)
heatmap_tool() (in module lib5c.tools.heatmap)
hic_extract_tool() (in module lib5c.tools.hic_extract)
I
iced_balance_matrix() (in module lib5c.contrib.iced.balancing)
iced_tool() (in module lib5c.tools.iced)
IcedTask (class in lib5c.contrib.luigi.tasks)
ident() (in module lib5c.algorithms.clustering.util)
identify_nearby_clusters() (in module lib5c.algorithms.clustering.util)
imputation_size (lib5c.contrib.luigi.tasks.IcedTask attribute)
(lib5c.contrib.luigi.tasks.KnightRuizTask attribute)
impute_values() (in module lib5c.util.counts)
in_boundaries() (in module lib5c.util.bedgraph)
infer_level_mapping() (in module lib5c.tools.helpers)
infer_replicate_names() (in module lib5c.tools.helpers)
interaction_score_tool() (in module lib5c.tools.interaction_score)
InteractionMatrix (class in lib5c.core.interactions)
InteractionMatrixOperator (class in lib5c.operators.base)
InteractionScoreTask (class in lib5c.contrib.luigi.tasks)
InteractionTrimmer (class in lib5c.operators.trimming)
interpolate_expected() (in module lib5c.algorithms.expected)
inverse_weighting_function() (in module lib5c.algorithms.filtering.filter_functions)
inverse_weights (lib5c.contrib.luigi.tasks.FilteringTask attribute)
iterative_spline_normalization() (in module lib5c.algorithms.spline_normalization)
J
joint_express_normalize() (in module lib5c.algorithms.express)
JointExpressInnerTask (class in lib5c.contrib.luigi.pipeline)
JointInnerMixin (class in lib5c.contrib.luigi.pipeline)
JointInnerParallelMixin (class in lib5c.contrib.luigi.pipeline)
JointTask (class in lib5c.contrib.luigi.pipeline)
K
kappa() (in module lib5c.algorithms.thresholding)
kappa_confusion_outfile (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
KnightRuizTask (class in lib5c.contrib.luigi.tasks)
knots (lib5c.contrib.luigi.tasks.SplineTask attribute)
kr_balance() (in module lib5c.algorithms.knight_ruiz)
kr_balance_matrix() (in module lib5c.algorithms.knight_ruiz)
kr_tool() (in module lib5c.tools.kr)
L
label_cluster() (lib5c.plotters.extendable.cluster_extendable_heatmap.ClusterExtendableHeatmap method)
label_connected_components() (in module lib5c.algorithms.thresholding)
LegacyPvaluesOneTask (class in lib5c.contrib.luigi.tasks)
LegacyPvaluesTwoTask (class in lib5c.contrib.luigi.tasks)
LegacyVisualizeFitTask (class in lib5c.contrib.luigi.tasks)
LegacyVisualizeVarianceTask (class in lib5c.contrib.luigi.tasks)
LegendExtendableHeatmap (class in lib5c.plotters.extendable.legend_extendable_heatmap)
lib5c (module)
lib5c.algorithms (module)
lib5c.algorithms.clustering (module)
lib5c.algorithms.clustering.adjacency (module)
lib5c.algorithms.clustering.enclave (module)
lib5c.algorithms.clustering.greedy (module)
lib5c.algorithms.clustering.knn (module)
lib5c.algorithms.clustering.quasicontiguity (module)
lib5c.algorithms.clustering.util (module)
lib5c.algorithms.clustering.valley (module)
lib5c.algorithms.convergency (module)
lib5c.algorithms.correlation (module)
lib5c.algorithms.determine_bins (module)
lib5c.algorithms.donut_filters (module)
lib5c.algorithms.enrichment (module)
lib5c.algorithms.expected (module)
lib5c.algorithms.express (module)
lib5c.algorithms.filtering (module)
lib5c.algorithms.filtering.bin_bin_filtering (module)
lib5c.algorithms.filtering.filter_functions (module)
lib5c.algorithms.filtering.fragment_bin_filtering (module)
lib5c.algorithms.filtering.fragment_fragment_filtering (module)
lib5c.algorithms.filtering.unsmoothable_columns (module)
lib5c.algorithms.filtering.util (module)
lib5c.algorithms.knight_ruiz (module)
lib5c.algorithms.outliers (module)
lib5c.algorithms.pca (module)
lib5c.algorithms.qnorm (module)
lib5c.algorithms.spline_normalization (module)
lib5c.algorithms.thresholding (module)
lib5c.algorithms.trimming (module)
lib5c.algorithms.variance (module)
lib5c.algorithms.variance.combined (module)
lib5c.algorithms.variance.cross_rep (module)
lib5c.algorithms.variance.deviation (module)
lib5c.algorithms.variance.estimate_variance (module)
lib5c.algorithms.variance.local (module)
lib5c.algorithms.variance.lognorm_dispersion (module)
lib5c.algorithms.variance.mle (module)
lib5c.algorithms.variance.nbinom_dispersion (module)
lib5c.contrib (module)
lib5c.contrib.iced (module)
lib5c.contrib.iced.balancing (module)
lib5c.contrib.interlap (module)
lib5c.contrib.interlap.util (module)
lib5c.contrib.luigi (module)
lib5c.contrib.luigi.config (module)
lib5c.contrib.luigi.pipeline (module)
lib5c.contrib.luigi.tasks (module)
lib5c.contrib.pybigwig (module)
lib5c.contrib.pybigwig.bigwig (module)
lib5c.contrib.seaborn (module)
lib5c.core (module)
lib5c.core.interactions (module)
lib5c.core.loci (module)
lib5c.core.mixins (module)
lib5c.operators (module)
lib5c.operators.base (module)
lib5c.operators.modeling (module)
lib5c.operators.qnorm (module)
lib5c.operators.standardization (module)
lib5c.operators.trimming (module)
lib5c.parsers (module)
lib5c.parsers.bed (module)
lib5c.parsers.bias (module)
lib5c.parsers.config (module)
lib5c.parsers.counts (module)
lib5c.parsers.genes (module)
lib5c.parsers.hic (module)
lib5c.parsers.loops (module)
lib5c.parsers.primer_names (module)
lib5c.parsers.primers (module)
lib5c.parsers.scaled (module)
lib5c.parsers.table (module)
lib5c.parsers.util (module)
lib5c.plotters (module)
lib5c.plotters.asymmetric_colormap (module)
lib5c.plotters.bias_heatmaps (module)
lib5c.plotters.boxplots (module)
lib5c.plotters.clustering (module)
lib5c.plotters.colormaps (module)
lib5c.plotters.colorscales (module)
lib5c.plotters.convergency (module)
lib5c.plotters.correlation (module)
lib5c.plotters.curve_fits (module)
lib5c.plotters.distance_dependence (module)
lib5c.plotters.distribution (module)
lib5c.plotters.enrichment (module)
lib5c.plotters.expected (module)
lib5c.plotters.extendable (module)
lib5c.plotters.extendable.base_extendable_heatmap (module)
lib5c.plotters.extendable.bed_extendable_heatmap (module)
lib5c.plotters.extendable.chipseq_extendable_heatmap (module)
lib5c.plotters.extendable.cluster_extendable_heatmap (module)
lib5c.plotters.extendable.domain_extendable_heatmap (module)
lib5c.plotters.extendable.extendable_figure (module)
lib5c.plotters.extendable.extendable_heatmap (module)
lib5c.plotters.extendable.gene_extendable_heatmap (module)
lib5c.plotters.extendable.legend_extendable_heatmap (module)
lib5c.plotters.extendable.motif_extendable_heatmap (module)
lib5c.plotters.extendable.rectangle_extendable_heatmap (module)
lib5c.plotters.extendable.ruler_extendable_heatmap (module)
lib5c.plotters.extendable.snp_extendable_heatmap (module)
lib5c.plotters.fits (module)
lib5c.plotters.heatmap (module)
lib5c.plotters.matrix (module)
lib5c.plotters.pca (module)
lib5c.plotters.queried_counts_heatmap (module)
lib5c.plotters.scatter (module)
lib5c.plotters.splines (module)
lib5c.plotters.variance (module)
lib5c.structures (module)
lib5c.structures.dataset (module)
lib5c.tools (module)
lib5c.tools.bias_heatmap (module)
lib5c.tools.bin (module)
lib5c.tools.boxplot (module)
lib5c.tools.colorscale (module)
lib5c.tools.convergency (module)
lib5c.tools.correlation (module)
lib5c.tools.dd_curve (module)
lib5c.tools.determine_bins (module)
lib5c.tools.distribution (module)
lib5c.tools.divide (module)
lib5c.tools.enrichment (module)
lib5c.tools.expected (module)
lib5c.tools.express (module)
lib5c.tools.heatmap (module)
lib5c.tools.helpers (module)
lib5c.tools.hic_extract (module)
lib5c.tools.iced (module)
lib5c.tools.interaction_score (module)
lib5c.tools.kr (module)
lib5c.tools.lib5c_toolbox (module)
lib5c.tools.log (module)
lib5c.tools.outliers (module)
lib5c.tools.parents (module)
lib5c.tools.pca (module)
lib5c.tools.pipeline (module)
lib5c.tools.pvalue_histogram (module)
lib5c.tools.pvalues (module)
lib5c.tools.qnorm (module)
lib5c.tools.qvalues (module)
lib5c.tools.remove (module)
lib5c.tools.smooth (module)
lib5c.tools.spline (module)
lib5c.tools.subtract (module)
lib5c.tools.threshold (module)
lib5c.tools.trim (module)
lib5c.tools.variance (module)
lib5c.tools.visualize_fits (module)
lib5c.tools.visualize_splines (module)
lib5c.tools.visualize_variance (module)
lib5c.util (module)
lib5c.util.annotationmap (module)
lib5c.util.ast_eval (module)
lib5c.util.bed (module)
lib5c.util.bedgraph (module)
lib5c.util.config (module)
lib5c.util.counts (module)
lib5c.util.counts_superdict (module)
lib5c.util.demo_data (module)
lib5c.util.dictionaries (module)
lib5c.util.distributions (module)
lib5c.util.donut (module)
lib5c.util.grouping (module)
lib5c.util.lowess (module)
lib5c.util.lru_cache (module)
lib5c.util.mathematics (module)
lib5c.util.metrics (module)
lib5c.util.optimization (module)
lib5c.util.parallelization (module)
lib5c.util.plotting (module)
lib5c.util.pretty_decorator (module)
lib5c.util.primers (module)
lib5c.util.sampling (module)
lib5c.util.scales (module)
lib5c.util.slicing (module)
lib5c.util.sorting (module)
lib5c.util.statistics (module)
lib5c.util.stratification (module)
lib5c.util.system (module)
lib5c.util.table (module)
lib5c.writers (module)
lib5c.writers.bedgraph (module)
lib5c.writers.bias (module)
lib5c.writers.config (module)
lib5c.writers.correlation (module)
lib5c.writers.counts (module)
lib5c.writers.hic (module)
lib5c.writers.pca (module)
lib5c.writers.primers (module)
lib5c.writers.table (module)
lib5c.writers.wustl (module)
lib5c_toolbox() (in module lib5c.tools.lib5c_toolbox)
load() (lib5c.structures.dataset.Dataset class method)
load_bias_vector() (in module lib5c.parsers.bias)
load_cis_trans_counts() (in module lib5c.parsers.counts)
load_counts() (in module lib5c.parsers.counts)
load_counts_by_name() (in module lib5c.parsers.counts)
load_counts_legacy() (in module lib5c.parsers.counts)
load_features() (in module lib5c.parsers.bed)
load_gene_table() (in module lib5c.parsers.genes)
load_genes() (in module lib5c.parsers.genes)
load_loops() (in module lib5c.parsers.loops)
load_primermap() (in module lib5c.parsers.primers)
load_range_from_contact_matrix() (in module lib5c.parsers.hic)
load_scaled() (in module lib5c.parsers.scaled)
load_table() (in module lib5c.parsers.table)
local_variance() (in module lib5c.algorithms.variance.local)
Locus (class in lib5c.core.loci)
locus_fold_threshold_lower (lib5c.operators.trimming.InteractionTrimmer attribute)
locus_fold_threshold_upper (lib5c.operators.trimming.InteractionTrimmer attribute)
locus_info_task() (lib5c.contrib.luigi.pipeline.TreeMixin method)
locus_list (lib5c.core.loci.LocusMap attribute)
locus_percentage_threshold_lower (lib5c.operators.trimming.InteractionTrimmer attribute)
locus_percentage_threshold_upper (lib5c.operators.trimming.InteractionTrimmer attribute)
LocusMap (class in lib5c.core.loci)
locusmap (lib5c.core.interactions.InteractionMatrix attribute)
LocusTrimmer (class in lib5c.operators.trimming)
log (lib5c.contrib.luigi.tasks.DistributionTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
(lib5c.contrib.luigi.tasks.PvalueTask attribute)
(lib5c.core.mixins.Loggable attribute)
log_base (lib5c.contrib.luigi.tasks.LogTask attribute)
log_donut (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
log_event() (lib5c.core.mixins.Loggable method)
log_parameters() (in module lib5c.util.distributions)
log_regional_counts() (in module lib5c.util.counts)
log_tool() (in module lib5c.tools.log)
log_transform (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
Loggable (class in lib5c.core.mixins)
LogTask (class in lib5c.contrib.luigi.tasks)
logx (lib5c.contrib.luigi.tasks.VarianceTask attribute)
logy (lib5c.contrib.luigi.tasks.VarianceTask attribute)
lower_left_filt() (in module lib5c.algorithms.donut_filters)
lower_left_footprint() (in module lib5c.util.donut)
lowess (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
lowess_agg() (in module lib5c.util.lowess)
lowess_binned() (in module lib5c.algorithms.expected)
lowess_binned_log_counts() (in module lib5c.algorithms.expected)
lowess_fit() (in module lib5c.util.lowess)
lowess_frac (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
lowess_log_log_binned() (in module lib5c.algorithms.expected)
lowess_log_log_fragment() (in module lib5c.algorithms.expected)
lru_cache() (in module lib5c.util.lru_cache)
M
main() (in module lib5c.parsers.bed)
(in module lib5c.parsers.counts)
(in module lib5c.parsers.genes)
(in module lib5c.parsers.primers)
(in module lib5c.parsers.scaled)
(in module lib5c.plotters.clustering)
(in module lib5c.util.annotationmap)
(in module lib5c.util.bed)
(in module lib5c.util.bedgraph)
(in module lib5c.util.demo_data)
(in module lib5c.util.parallelization)
(in module lib5c.util.scales)
(in module lib5c.writers.bedgraph)
(in module lib5c.writers.counts)
(in module lib5c.writers.wustl)
make_annotationmaps() (in module lib5c.util.annotationmap)
make_atlas() (in module lib5c.util.counts_superdict)
make_atlas_peaks() (in module lib5c.util.counts_superdict)
make_clusters() (in module lib5c.algorithms.clustering.adjacency)
(in module lib5c.algorithms.clustering.greedy)
(in module lib5c.algorithms.clustering.knn)
make_distance_matrix() (in module lib5c.algorithms.expected)
make_donut_selector() (in module lib5c.util.donut)
make_expected_dict_from_matrix() (in module lib5c.algorithms.expected)
make_expected_matrix() (in module lib5c.algorithms.expected)
make_expected_matrix_from_dict() (in module lib5c.algorithms.expected)
make_expected_matrix_from_list() (in module lib5c.algorithms.expected)
make_fflj_id_map() (in module lib5c.util.table)
make_filter_function() (in module lib5c.algorithms.filtering.filter_functions)
make_pairwise_correlation_matrix() (in module lib5c.algorithms.correlation)
make_pairwise_correlation_matrix_from_counts_matrix() (in module lib5c.algorithms.correlation)
make_poly_log_log_binned_expected_matrix() (in module lib5c.algorithms.expected)
make_poly_log_log_fragment_expected_matrix() (in module lib5c.algorithms.expected)
make_powerlaw_binned_expected_matrix() (in module lib5c.algorithms.expected)
make_pvalues_superdict() (in module lib5c.util.counts_superdict)
make_single_annotationmap() (in module lib5c.util.annotationmap)
make_zoom_window() (in module lib5c.plotters.clustering)
MakeBinned (class in lib5c.contrib.luigi.pipeline)
MakeCrossVariance (class in lib5c.contrib.luigi.pipeline)
MakeExpected (class in lib5c.contrib.luigi.pipeline)
MakeExpress (class in lib5c.contrib.luigi.pipeline)
MakeIced (class in lib5c.contrib.luigi.pipeline)
MakeInteractionScores (class in lib5c.contrib.luigi.pipeline)
MakeJointExpress (class in lib5c.contrib.luigi.pipeline)
MakeKR (class in lib5c.contrib.luigi.pipeline)
MakeLegacyPvaluesOne (class in lib5c.contrib.luigi.pipeline)
MakeLogged (class in lib5c.contrib.luigi.pipeline)
MakeObsMinusExp (class in lib5c.contrib.luigi.pipeline)
MakeObsOverExp (class in lib5c.contrib.luigi.pipeline)
MakePvalues (class in lib5c.contrib.luigi.pipeline)
MakeQnorm (class in lib5c.contrib.luigi.pipeline)
MakeQvalues (class in lib5c.contrib.luigi.pipeline)
MakeRaw (class in lib5c.contrib.luigi.pipeline)
MakeRemoved (class in lib5c.contrib.luigi.pipeline)
MakeSmoothed (class in lib5c.contrib.luigi.pipeline)
MakeSpline (class in lib5c.contrib.luigi.pipeline)
MakeThreshold (class in lib5c.contrib.luigi.pipeline)
MakeVariance (class in lib5c.contrib.luigi.pipeline)
matrix (lib5c.core.interactions.InteractionMatrix attribute)
matrix_to_counts_superdict() (in module lib5c.util.counts_superdict)
max_threshold (lib5c.operators.trimming.LocusTrimmer attribute)
max_with_lower_left (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
median() (in module lib5c.algorithms.filtering.filter_functions)
merge_clusters() (in module lib5c.algorithms.clustering.util)
merge_to_which() (in module lib5c.algorithms.clustering.adjacency)
(in module lib5c.algorithms.clustering.enclave)
method (lib5c.contrib.luigi.tasks.QvaluesTask attribute)
min_disp (lib5c.contrib.luigi.tasks.VarianceTask attribute)
min_dist (lib5c.contrib.luigi.tasks.VarianceTask attribute)
min_exp (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
min_obs (lib5c.contrib.luigi.tasks.VarianceTask attribute)
min_threshold (lib5c.operators.trimming.LocusTrimmer attribute)
mle_variance() (in module lib5c.algorithms.variance.mle)
mode (lib5c.contrib.luigi.tasks.DistributionTask attribute)
(lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask attribute)
model (lib5c.contrib.luigi.tasks.VarianceTask attribute)
model_outfile (lib5c.contrib.luigi.tasks.SplineTask attribute)
monotonic (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
MotifExtendableHeatmap (class in lib5c.plotters.extendable.motif_extendable_heatmap)
MultiInteractionMatrixOperator (class in lib5c.operators.base)
N
name_dict (lib5c.core.loci.LocusMap attribute)
name_to_index_dict (lib5c.core.loci.LocusMap attribute)
natural_sort_key() (in module lib5c.util.primers)
nb_nll() (in module lib5c.algorithms.variance.nbinom_dispersion)
nb_nll_derivative() (in module lib5c.algorithms.variance.nbinom_dispersion)
nb_pmf() (in module lib5c.algorithms.variance.nbinom_dispersion)
norm (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap attribute)
norm_counts() (in module lib5c.util.counts)
norm_filter_function() (in module lib5c.algorithms.filtering.filter_functions)
null_value() (in module lib5c.parsers.util)
O
outfile_pattern (lib5c.contrib.luigi.pipeline.JointTask attribute)
(lib5c.contrib.luigi.pipeline.RawCounts attribute)
(lib5c.contrib.luigi.pipeline.TreeMixin attribute)
(lib5c.contrib.luigi.tasks.QnormTask attribute)
outliers_tool() (in module lib5c.tools.outliers)
OutliersTask (class in lib5c.contrib.luigi.tasks)
outline_cluster() (lib5c.plotters.extendable.cluster_extendable_heatmap.ClusterExtendableHeatmap method)
outline_domain() (lib5c.plotters.extendable.domain_extendable_heatmap.DomainExtendableHeatmap method)
outline_domains() (lib5c.plotters.extendable.domain_extendable_heatmap.DomainExtendableHeatmap method)
output() (lib5c.contrib.luigi.pipeline.DetermineBins method)
(lib5c.contrib.luigi.pipeline.JointInnerParallelMixin method)
(lib5c.contrib.luigi.pipeline.JointTask method)
(lib5c.contrib.luigi.pipeline.MakeThreshold method)
(lib5c.contrib.luigi.pipeline.PrimerFile method)
(lib5c.contrib.luigi.pipeline.RawCounts method)
(lib5c.contrib.luigi.pipeline.TreeMixin method)
overwrite_value (lib5c.contrib.luigi.tasks.OutliersTask attribute)
P
p (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
pad_and_crop() (in module lib5c.util.donut)
parallel_divide_counts() (in module lib5c.util.counts)
parallel_log_counts() (in module lib5c.util.counts)
parallel_subtract_counts() (in module lib5c.util.counts)
parallel_unlog_counts() (in module lib5c.util.counts)
parallelize_reps() (in module lib5c.contrib.luigi.tasks)
parallelize_reps_regions() (in module lib5c.contrib.luigi.tasks)
parse_config() (in module lib5c.parsers.config)
(in module lib5c.util.config)
parse_feature_from_string() (in module lib5c.util.bed)
parse_field() (in module lib5c.parsers.util)
parse_range_string() (in module lib5c.tools.hic_extract)
pca_tool() (in module lib5c.tools.pca)
peaks_to_array_index() (in module lib5c.algorithms.clustering.util)
percentage_threshold_lower (lib5c.operators.trimming.LocusTrimmer attribute)
percentage_threshold_upper (lib5c.operators.trimming.LocusTrimmer attribute)
PerRepSimpleTreeMixin (class in lib5c.contrib.luigi.pipeline)
Picklable (class in lib5c.core.mixins)
pipeline_tool() (in module lib5c.tools.pipeline)
PipelineTask (class in lib5c.contrib.luigi.pipeline)
pixelmap (lib5c.structures.dataset.Dataset attribute)
plot_annotation_vs_annotation_heatmap() (in module lib5c.plotters.enrichment)
plot_bias_heatmap() (in module lib5c.plotters.bias_heatmaps)
plot_bin_expected() (in module lib5c.plotters.expected)
plot_cluster() (in module lib5c.plotters.clustering)
plot_cluster_indices() (in module lib5c.plotters.clustering)
plot_convergency() (in module lib5c.plotters.convergency)
plot_correlation_matrix() (in module lib5c.plotters.correlation)
plot_distance_dependence() (in module lib5c.plotters.distance_dependence)
plot_distance_dependence_parallel() (in module lib5c.plotters.distance_dependence)
plot_fit() (in module lib5c.plotters.curve_fits)
(in module lib5c.plotters.fits)
plot_fragment_expected() (in module lib5c.plotters.expected)
plot_global_distributions() (in module lib5c.plotters.distribution)
plot_group_fit() (in module lib5c.plotters.fits)
plot_heatmap() (in module lib5c.plotters.heatmap)
plot_log_log_expected() (in module lib5c.plotters.expected)
plot_looptype_vs_annotation_heatmap() (in module lib5c.plotters.enrichment)
plot_matrix() (in module lib5c.plotters.matrix)
plot_multi_pca() (in module lib5c.plotters.pca)
plot_mvr() (in module lib5c.plotters.variance)
plot_mvr_parallel() (in module lib5c.plotters.variance)
plot_outfile (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
plot_outfile_hexbin (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
plot_outfile_kde (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
plot_overlay_mvr() (in module lib5c.plotters.variance)
plot_pca() (in module lib5c.plotters.pca)
plot_queried_counts_heatmap() (in module lib5c.plotters.queried_counts_heatmap)
plot_regional_distribtions() (in module lib5c.plotters.distribution)
plot_regional_distribtions_parallel() (in module lib5c.plotters.distribution)
plot_regional_locus_boxplot() (in module lib5c.plotters.boxplots)
plot_stack_bargraph() (in module lib5c.plotters.enrichment)
poly_log_log_binned() (in module lib5c.algorithms.expected)
poly_log_log_fragment() (in module lib5c.algorithms.expected)
powerlaw (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
powerlaw_binned() (in module lib5c.algorithms.expected)
preceding_task() (lib5c.contrib.luigi.pipeline.TreeMixin method)
prepare_convergency_annotations() (in module lib5c.algorithms.convergency)
prepare_exp_var_for_plotting() (in module lib5c.plotters.variance)
prepare_exp_var_for_plotting_parallel() (in module lib5c.plotters.variance)
pretty_decorator() (in module lib5c.util.pretty_decorator)
PrimerFile (class in lib5c.contrib.luigi.pipeline)
primerfile (lib5c.contrib.luigi.pipeline.PrimerFile attribute)
print_log() (lib5c.core.mixins.Loggable method)
process_annotations() (in module lib5c.algorithms.enrichment)
propagate_nan (lib5c.operators.standardization.Standardizer attribute)
propagate_nans() (in module lib5c.util.counts)
pseudocount (lib5c.contrib.luigi.tasks.LogTask attribute)
pvalue_histogram_tool() (in module lib5c.tools.pvalue_histogram)
pvalues_tool() (in module lib5c.tools.pvalues)
PvalueTask (class in lib5c.contrib.luigi.tasks)
Q
qnorm() (in module lib5c.algorithms.qnorm)
qnorm_counts_superdict() (in module lib5c.algorithms.qnorm)
qnorm_fast() (in module lib5c.algorithms.qnorm)
qnorm_fast_parallel() (in module lib5c.algorithms.qnorm)
qnorm_parallel() (in module lib5c.algorithms.qnorm)
qnorm_tool() (in module lib5c.tools.qnorm)
QnormInnerTask (class in lib5c.contrib.luigi.pipeline)
QnormTask (class in lib5c.contrib.luigi.tasks)
quadratic_log_log_fit() (in module lib5c.util.optimization)
QuantileNormalizer (class in lib5c.operators.qnorm)
queried_counts_to_pvalues() (in module lib5c.util.counts)
query() (lib5c.contrib.pybigwig.bigwig.BigWig method)
query_interlap() (in module lib5c.contrib.interlap.util)
qvalues_tool() (in module lib5c.tools.qvalues)
QvaluesTask (class in lib5c.contrib.luigi.tasks)
R
rankdata_plus() (in module lib5c.util.sorting)
RawCounts (class in lib5c.contrib.luigi.pipeline)
RectangleExtendableHeatmap (class in lib5c.plotters.extendable.rectangle_extendable_heatmap)
reduce_bedgraph() (in module lib5c.util.bedgraph)
reduced_get() (in module lib5c.util.dictionaries)
reference (lib5c.contrib.luigi.pipeline.MakeQnorm attribute)
(lib5c.contrib.luigi.tasks.QnormTask attribute)
region (lib5c.contrib.luigi.tasks.RegionalTaskMixin attribute)
region_index_dict (lib5c.core.loci.LocusMap attribute)
regional (lib5c.contrib.luigi.pipeline.MakeQnorm attribute)
(lib5c.contrib.luigi.tasks.QnormTask attribute)
(lib5c.contrib.luigi.tasks.VarianceTask attribute)
regional_counts_to_pvalues() (in module lib5c.util.counts)
RegionalTaskMixin (class in lib5c.contrib.luigi.tasks)
regions (lib5c.core.loci.LocusMap attribute)
regression (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
remove_high_spatial_outliers() (in module lib5c.algorithms.outliers)
remove_primer_primer_pairs() (in module lib5c.algorithms.outliers)
remove_tool() (in module lib5c.tools.remove)
rep (lib5c.contrib.luigi.pipeline.JointTask attribute)
(lib5c.contrib.luigi.pipeline.RawCounts attribute)
(lib5c.contrib.luigi.pipeline.TreeMixin attribute)
repinfo (lib5c.structures.dataset.Dataset attribute)
requires() (lib5c.contrib.luigi.pipeline.DetermineBins method)
(lib5c.contrib.luigi.pipeline.JointInnerMixin method)
(lib5c.contrib.luigi.pipeline.JointTask method)
(lib5c.contrib.luigi.pipeline.MakeBinned method)
(lib5c.contrib.luigi.pipeline.MakeCrossVariance method)
(lib5c.contrib.luigi.pipeline.MakeLegacyPvaluesOne method)
(lib5c.contrib.luigi.pipeline.MakeObsMinusExp method)
(lib5c.contrib.luigi.pipeline.MakeObsOverExp method)
(lib5c.contrib.luigi.pipeline.MakePvalues method)
(lib5c.contrib.luigi.pipeline.MakeVariance method)
(lib5c.contrib.luigi.pipeline.PerRepSimpleTreeMixin method)
(lib5c.contrib.luigi.pipeline.PipelineTask method)
reshape_cluster_array_to_dict() (in module lib5c.algorithms.clustering.util)
resolve_expected_models() (in module lib5c.tools.helpers)
resolve_level() (in module lib5c.tools.helpers)
resolve_parallel() (in module lib5c.tools.helpers)
resolve_primerfile() (in module lib5c.tools.helpers)
RulerExtendableHeatmap (class in lib5c.plotters.extendable.ruler_extendable_heatmap)
run() (lib5c.contrib.luigi.pipeline.MakeJointExpress method)
(lib5c.contrib.luigi.pipeline.MakeQnorm method)
(lib5c.contrib.luigi.pipeline.MakeRaw method)
(lib5c.contrib.luigi.tasks.BinTask method)
(lib5c.contrib.luigi.tasks.CmdTask method)
(lib5c.contrib.luigi.tasks.DivideTask method)
(lib5c.contrib.luigi.tasks.ExpectedTask method)
(lib5c.contrib.luigi.tasks.ExpressTask method)
(lib5c.contrib.luigi.tasks.IcedTask method)
(lib5c.contrib.luigi.tasks.InteractionScoreTask method)
(lib5c.contrib.luigi.tasks.KnightRuizTask method)
(lib5c.contrib.luigi.tasks.LegacyPvaluesOneTask method)
(lib5c.contrib.luigi.tasks.LegacyPvaluesTwoTask method)
(lib5c.contrib.luigi.tasks.OutliersTask method)
(lib5c.contrib.luigi.tasks.PvalueTask method)
(lib5c.contrib.luigi.tasks.QnormTask method)
(lib5c.contrib.luigi.tasks.QvaluesTask method)
(lib5c.contrib.luigi.tasks.SmoothTask method)
(lib5c.contrib.luigi.tasks.SplineTask method)
(lib5c.contrib.luigi.tasks.SubtractTask method)
(lib5c.contrib.luigi.tasks.ThresholdTask method)
S
save() (lib5c.plotters.extendable.extendable_figure.ExtendableFigure method)
(lib5c.structures.dataset.Dataset method)
scatter() (in module lib5c.plotters.scatter)
select() (lib5c.structures.dataset.Dataset method)
set_cis_trans_nans() (in module lib5c.parsers.counts)
set_data() (lib5c.core.mixins.Annotatable method)
set_nans() (in module lib5c.parsers.counts)
set_value() (lib5c.core.mixins.Annotatable method)
shell_quote() (in module lib5c.util.system)
shifted_colormap() (in module lib5c.plotters.asymmetric_colormap)
significance_threshold (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
simple_sum() (in module lib5c.algorithms.filtering.filter_functions)
size() (lib5c.core.interactions.InteractionMatrix method)
(lib5c.core.loci.LocusMap method)
size_filter() (in module lib5c.algorithms.thresholding)
size_threshold (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
slice_matrix_by_grange() (in module lib5c.util.slicing)
smooth_tool() (in module lib5c.tools.smooth)
SmoothTask (class in lib5c.contrib.luigi.tasks)
SNPExtendableHeatmap (class in lib5c.plotters.extendable.snp_extendable_heatmap)
source (lib5c.contrib.luigi.tasks.CrossVarianceTask attribute)
(lib5c.contrib.luigi.tasks.VarianceTask attribute)
spline_tool() (in module lib5c.tools.spline)
SplineTask (class in lib5c.contrib.luigi.tasks)
split_cluster() (in module lib5c.algorithms.clustering.quasicontiguity)
(in module lib5c.algorithms.clustering.valley)
split_clusters() (in module lib5c.algorithms.clustering.quasicontiguity)
(in module lib5c.algorithms.clustering.valley)
split_self_regionally() (in module lib5c.tools.helpers)
splitall() (in module lib5c.util.system)
Standardizer (class in lib5c.operators.standardization)
start (lib5c.core.loci.Locus attribute)
stouffer() (in module lib5c.util.statistics)
strip_zero_rows_columns_sym_mat() (in module lib5c.algorithms.knight_ruiz)
subtract_regional_counts() (in module lib5c.util.counts)
subtract_tool() (in module lib5c.tools.subtract)
SubtractTask (class in lib5c.contrib.luigi.tasks)
sum_threshold_lower (lib5c.operators.trimming.LocusTrimmer attribute)
sum_threshold_upper (lib5c.operators.trimming.LocusTrimmer attribute)
symmetrize() (in module lib5c.util.mathematics)
T
table (lib5c.contrib.luigi.pipeline.PipelineTask attribute)
(lib5c.contrib.luigi.pipeline.TreeMixin attribute)
tasks (lib5c.contrib.luigi.pipeline.PipelineTask attribute)
test_function_four() (in module lib5c.util.parallelization)
test_function_one() (in module lib5c.util.parallelization)
test_function_three() (in module lib5c.util.parallelization)
test_function_two() (in module lib5c.util.parallelization)
threshold (lib5c.contrib.luigi.tasks.FilteringTask attribute)
threshold_tool() (in module lib5c.tools.threshold)
ThresholdTask (class in lib5c.contrib.luigi.tasks)
tie (lib5c.operators.qnorm.QuantileNormalizer attribute)
to_bedfile() (lib5c.core.loci.LocusMap method)
to_countsfile() (lib5c.core.interactions.InteractionMatrix method)
to_pickle() (lib5c.core.mixins.Picklable method)
tolerance (lib5c.contrib.luigi.tasks.LegacyVisualizeFitTask attribute)
transform_coord() (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap method)
transform_feature() (lib5c.plotters.extendable.base_extendable_heatmap.BaseExtendableHeatmap method)
TreeMixin (class in lib5c.contrib.luigi.pipeline)
trim_counts() (in module lib5c.algorithms.trimming)
trim_counts_superdict() (in module lib5c.algorithms.trimming)
trim_primers() (in module lib5c.algorithms.trimming)
trim_tool() (in module lib5c.tools.trim)
two_tail (lib5c.contrib.luigi.tasks.ThresholdTask attribute)
two_way_thresholding() (in module lib5c.algorithms.thresholding)
U
unflatten() (lib5c.core.interactions.InteractionMatrix method)
unflatten_cis() (lib5c.core.interactions.InteractionMatrix method)
unflatten_counts() (in module lib5c.util.counts)
unflatten_counts_from_list() (in module lib5c.util.counts)
unflatten_regional_counts() (in module lib5c.util.counts)
uniform_range_coverage_sample() (in module lib5c.util.sampling)
unlog (lib5c.contrib.luigi.tasks.LogTask attribute)
unlog_regional_counts() (in module lib5c.util.counts)
unsmoothable_column_threshold_heuristic() (in module lib5c.algorithms.filtering.unsmoothable_columns)
V
value_filter_function() (in module lib5c.algorithms.filtering.filter_functions)
value_threshold_lower (lib5c.operators.trimming.InteractionTrimmer attribute)
value_threshold_upper (lib5c.operators.trimming.InteractionTrimmer attribute)
variance_to_dispersion() (in module lib5c.algorithms.variance.lognorm_dispersion)
(in module lib5c.algorithms.variance.nbinom_dispersion)
variance_tool() (in module lib5c.tools.variance)
VarianceTask (class in lib5c.contrib.luigi.tasks)
visualizable() (in module lib5c.contrib.luigi.tasks)
visualize_fits_tool() (in module lib5c.tools.visualize_fits)
visualize_spline() (in module lib5c.plotters.splines)
visualize_splines_tool() (in module lib5c.tools.visualize_splines)
visualize_variance_tool() (in module lib5c.tools.visualize_variance)
vst (lib5c.contrib.luigi.tasks.PvalueTask attribute)
W
w (lib5c.contrib.luigi.tasks.ExpectedTask attribute)
weighted_amean() (in module lib5c.algorithms.filtering.filter_functions)
weighted_gmean() (in module lib5c.algorithms.filtering.filter_functions)
weighted_values_distances_function() (in module lib5c.algorithms.filtering.filter_functions)
window_function (lib5c.contrib.luigi.tasks.FilteringTask attribute)
window_size (lib5c.contrib.luigi.tasks.OutliersTask attribute)
window_width (lib5c.contrib.luigi.tasks.FilteringTask attribute)
wipe_counts() (in module lib5c.algorithms.trimming)
wipe_counts_superdict() (in module lib5c.algorithms.trimming)
wipe_prebinned_unsmoothable_columns() (in module lib5c.algorithms.filtering.unsmoothable_columns)
wipe_unsmoothable_columns (lib5c.contrib.luigi.tasks.FilteringTask attribute)
wipe_unsmoothable_columns() (in module lib5c.algorithms.filtering.unsmoothable_columns)
write_bedgraph() (in module lib5c.writers.bedgraph)
write_cis_bias_vector() (in module lib5c.writers.bias)
write_cis_trans_counts() (in module lib5c.writers.counts)
write_config() (in module lib5c.writers.config)
write_correlation_table() (in module lib5c.writers.correlation)
write_counts() (in module lib5c.writers.counts)
write_pca() (in module lib5c.writers.pca)
write_pixelmap_legacy() (in module lib5c.writers.primers)
write_primermap() (in module lib5c.writers.primers)
write_rao_matrix() (in module lib5c.writers.hic)
write_table() (in module lib5c.writers.table)
write_wustl() (in module lib5c.writers.wustl)
X
x_unit (lib5c.contrib.luigi.tasks.VarianceTask attribute)
Y
y_unit (lib5c.contrib.luigi.tasks.VarianceTask attribute)
Z
zero_nans() (in module lib5c.util.mathematics)
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