Index

Symbols

--alignments epiout command line option --bed epiannot command line option epiout command line option --bottleneck_size epiout command line option --ccres epiannot_create command line option --chrom_sizes epiannot command line option --config epiannot command line option --confounders epiout command line option --cores epiout command line option, [1] --count_table epiout command line option --counts epiannot command line option --file_format epiout command line option --gene_types epiannot command line option --gtf epiannot command line option

--hic epiannot_create command line option --hic_bin_vicinity epiannot command line option --hic_binsize epiannot command line option --hic_min_read epiannot command line option --hic_normalization epiannot command line option --mapq epiout command line option --min_count epiout command line option --min_percent_sample epiout command line option --output_dir epiannot_create command line option --output_prefix epiannot command line option epiout command line option, [1] --subset_chrom epiout command line option --tf epiannot_create command line option --tissue epiannot_create command line option

_

__call__() (epiout.autoencoder.LinearAutoEncoder method) (epiout.epiout.EpiOut method) __eq__() (epiout.dataclasses.Peak method) __len__() (epiout.dataclasses.Peak method) __repr__() (epiout.dataclasses.Peak method) __str__() (epiout.dataclasses.Peak method) _abc_score() (epiout.annotate.EpiAnnot method) _annotate_feature() (epiout.annotate.EpiAnnot method) _annotate_grs() (epiout.annotate.EpiAnnot method) _chipseq_marks() (epiout.annotate.EpiAnnot method) _co_outliers() (epiout.annotate.EpiAnnot method) _count_samples() (epiout.dataset.EpiOutDataset method) _df() (epiout.result.EpiOutResult method) _distal_gene() (epiout.gene.GeneLink method) _encode_bed_url (in module epiout.annotation_config) _encode_hic_url (in module epiout.annotation_config) _fill() (epiout.plot.CoveragePlot method) _filters() (epiout.dataset.EpiOutDataset static method) _fit() (epiout.optimizer.BackwardLineSearchGD method) _has_chipseq() (epiout.annotate.EpiAnnot method) _hyperparam() (epiout.epiout.EpiOut method) _infer_dispersion_mle() (epiout.negative_binomial.NegativeBinomial method) _infer_dispersion_mom() (epiout.negative_binomial.NegativeBinomial method) _infer_mean_mom() (epiout.negative_binomial.NegativeBinomial method) _label() (epiout.plot.CoveragePlot method) _line_search() (epiout.optimizer.BackwardLineSearchGD method) _line_search_cond() (epiout.optimizer.BackwardLineSearchGD method) _LineSearchResult (in module epiout.optimizer)

_LineSearchStep (in module epiout.optimizer) _log_prob() (epiout.negative_binomial.NegativeBinomial static method) _loss_grad() (epiout.optimizer.BackwardLineSearchGD method) _loss_grad_decoder() (epiout.autoencoder.LinearAutoEncoder method) _loss_grad_encoder() (epiout.autoencoder.LinearAutoEncoder method) _lr_decay() (epiout.optimizer.BackwardLineSearchGD method) _melt() (epiout.gene.GeneLink method) _neighbors() (epiout.annotate.EpiAnnot method) _peak_gene() (epiout.gene.GeneLink method) _peak_str() (in module epiout.utils.utils) _promoter_gene() (epiout.gene.GeneLink method) _promoters() (epiout.gene.GeneLink method) _proximal_gene() (epiout.gene.GeneLink method) _read() (epiout.annotate.EpiAnnot method) (epiout.annotation_config.AnnotationConfig method) (in module epiout.annotation_config) _read_bed() (epiout.annotate.EpiAnnot method) _read_chrom_sizes() (epiout.hic.HicReader static method) _read_contacts() (epiout.hic.HicReader method) _read_counts() (epiout.annotate.EpiAnnot method) _rlnorm() (in module epiout.inject) _tss_proximal() (epiout.annotate.EpiAnnot method) _update() (epiout.optimizer.BackwardLineSearchGD method) _update_decoder() (epiout.autoencoder.LinearAutoEncoder method) _update_encoder() (epiout.autoencoder.LinearAutoEncoder method) _valid_alignments() (epiout.dataset.EpiOutDataset static method) _valid_bed() (epiout.dataset.EpiOutDataset static method) _validate() (epiout.annotation_config.AnnotationConfig method) _wilfe_condition() (epiout.optimizer.BackwardLineSearchGD method)

A

annotate() (epiout.annotate.EpiAnnot method) (epiout.annotate.GTFAnnot method)

annotate_hic() (epiout.annotate.EpiAnnot method) AnnotationConfig (class in epiout.annotation_config)

B

backward_linesearch_gd() (in module epiout.optimizer)

BackwardLineSearchGD (class in epiout.optimizer)

C

call() (epiout.negative_binomial.NBLoss method) ccres_urls (in module epiout.annotation_config) center (epiout.dataclasses.Peak property) chrom (epiout.dataclasses.Peak property) chroms (in module epiout.utils.common) cli_epiannot() (in module epiout.main) cli_epiannot_create() (in module epiout.main) cli_epiannot_list() (in module epiout.main) cli_epicount() (in module epiout.main) cli_epiout() (in module epiout.main) contact_scores() (epiout.hic.HicReader method)

copy() (epiout.dataclasses.Peak method) count() (epiout.dataset.EpiOutDataset method) count_reads() (epiout.dataset.EpiOutDataset static method) counts (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property) counts_mean (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property) CountsPlot (class in epiout.plot) coverage_bigwig() (in module epiout.plot) CoveragePlot (class in epiout.plot) create_config() (in module epiout.annotation_config)

D

data() (epiout.plot.CountsPlot method) (epiout.plot.CoveragePlot method) (epiout.plot.QQPlot method) (epiout.plot.RankPlot method) (epiout.plot.VolconaPlot method)

df_batch_writer() (in module epiout.utils) (in module epiout.utils.io) distal_features() (epiout.gene.GeneLink method) distal_gene() (epiout.gene.GeneLink method) download_ccres() (in module epiout.annotation_config)

E

encode_metadata() (epiout.epiout.EpiOut method) end (epiout.dataclasses.Peak property) EpiAnnot (class in epiout.annotate) epiannot command line option --bed --chrom_sizes --config --counts --gene_types --gtf --hic_bin_vicinity --hic_binsize --hic_min_read --hic_normalization --output_prefix epiannot_create command line option --ccres --hic --output_dir --tf --tissue epiout module EpiOut (class in epiout.epiout) epiout command line option --alignments --bed --bottleneck_size --confounders --cores, [1] --count_table --file_format --mapq --min_count --min_percent_sample --output_prefix, [1] --subset_chrom epiout.annotate module

epiout.annotation_config module epiout.autoencoder module epiout.dataclasses module epiout.dataset module epiout.epiout module epiout.gene module epiout.hic module epiout.inject module epiout.main module epiout.negative_binomial module epiout.optimizer module epiout.plot module epiout.result module epiout.sflognorm module epiout.utils module epiout.utils.common module epiout.utils.genomic_features module epiout.utils.io module epiout.utils.utils module EpiOutDataset (class in epiout.dataset) EpiOutResult (class in epiout.result)

F

features() (epiout.gene.GeneLink method) fit() (epiout.autoencoder.LinearAutoEncoder method) (epiout.optimizer.BackwardLineSearchGD method) (epiout.sflognorm.SFLogNorm method)

fit_transform() (epiout.sflognorm.SFLogNorm method) from_dict() (epiout.annotation_config.AnnotationConfig class method) from_str() (epiout.dataclasses.Peak class method)

G

GeneLink (class in epiout.gene)

GTFAnnot (class in epiout.annotate)

H

HicReader (class in epiout.hic)

I

import_hicstraw() (in module epiout.hic) import_onnxruntime() (in module epiout.gene) infer_dispersion() (epiout.negative_binomial.NegativeBinomial method)

infer_mean() (epiout.negative_binomial.NegativeBinomial method) init_weights() (epiout.autoencoder.LinearAutoEncoder method) inject_outliers() (in module epiout.inject) inverse_transform() (epiout.sflognorm.SFLogNorm method)

L

l2fc (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property) line_search() (epiout.optimizer.BackwardLineSearchGD method) LinearAutoEncoder (class in epiout.autoencoder) load() (epiout.result.EpiOutResult class method)

log_padj (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property) log_prob() (epiout.autoencoder.LinearAutoEncoder method) (epiout.negative_binomial.NegativeBinomial method) logit() (in module epiout.utils)

M

match_chrom() (epiout.hic.HicReader static method) module epiout epiout.annotate epiout.annotation_config epiout.autoencoder epiout.dataclasses epiout.dataset epiout.epiout epiout.gene epiout.hic epiout.inject epiout.main epiout.negative_binomial epiout.optimizer epiout.plot epiout.result epiout.sflognorm epiout.utils epiout.utils.common epiout.utils.genomic_features epiout.utils.io epiout.utils.utils

N

nb (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property)

NBLoss (class in epiout.negative_binomial) NegativeBinomial (class in epiout.negative_binomial)

O

outlier (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property)

P

padj (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property) Peak (class in epiout.dataclasses) peak_str() (in module epiout.utils) (in module epiout.utils.utils) plot() (epiout.plot.CountsPlot method) (epiout.plot.CoveragePlot method) (epiout.plot.QQPlot method) (epiout.plot.RankPlot method) (epiout.plot.VolconaPlot method) plot_corr_heatmap() (epiout.result.EpiOutResult method) (in module epiout.plot) plot_counts() (epiout.result.EpiOutResult method) (in module epiout.plot) plot_coverage() (in module epiout.plot)

plot_coverage_line() (in module epiout.plot) plot_rank() (epiout.result.EpiOutResult method) (in module epiout.plot) plot_umap() (epiout.result.EpiOutResult method) (in module epiout.plot) plot_volcona() (epiout.result.EpiOutResult method) (in module epiout.plot) predict() (epiout.gene.GeneLink method) promoter_features() (epiout.gene.GeneLink method) promoter_gene() (epiout.gene.GeneLink method) proximal_features() (epiout.gene.GeneLink method) proximal_gene() (epiout.gene.GeneLink method) pval (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property) pval() (epiout.negative_binomial.NegativeBinomial method)

Q

qq_plot() (epiout.result.EpiOutResult method) (in module epiout.plot)

QQPlot (class in epiout.plot)

R

RankPlot (class in epiout.plot) read_alignments() (epiout.dataset.EpiOutDataset method) read_bed() (epiout.dataset.EpiOutDataset method) read_features() (epiout.annotate.GTFAnnot method)

read_hic() (in module epiout.annotation_config) read_histone() (in module epiout.annotation_config) read_tf() (in module epiout.annotation_config) results() (epiout.result.EpiOutResult method) results_all() (epiout.result.EpiOutResult method)

S

save() (epiout.result.EpiOutResult method) save_annotate() (epiout.annotate.EpiAnnot method) sflog() (epiout.sflognorm.SFLogNorm static method)

SFLogNorm (class in epiout.sflognorm) size_factor() (epiout.sflognorm.SFLogNorm static method) start (epiout.dataclasses.Peak property)

T

tes_genes() (in module epiout.utils.genomic_features) to_dict() (epiout.annotation_config.AnnotationConfig method) transform() (epiout.sflognorm.SFLogNorm method)

trim_mean() (in module epiout.utils) tss_genes() (in module epiout.utils.genomic_features) tune_bottleneck() (epiout.epiout.EpiOut method)

U

update_decoder() (epiout.autoencoder.LinearAutoEncoder method)

update_dispersion() (epiout.autoencoder.LinearAutoEncoder method) update_encoder() (epiout.autoencoder.LinearAutoEncoder method)

V

VolconaPlot (class in epiout.plot)

W

width (epiout.dataclasses.Peak property)

Z

zscore (epiout.result.EpiOutResult attribute) (epiout.result.EpiOutResult property)