Index

_

__init__() (BAMReader method) (ChrLevels method) (Metagene method) (MetageneFiles method) (PivotRegion method) (UniversalBatch method) (UniversalReader method) (UniversalReplicatesReader method) (UniversalWriter method)

A

all() (ClusterMany method) (ClusterSingle method) (Genome method)

append_metagene() (PCA method)

B

BAMReader (class in bsxplorer) batch_size (UniversalReader property) BinomialData (class in bsxplorer)

box_plot() (ChrLevels method) (MetageneFiles method) BoxPlot (class in bsxplorer)

C

categorise() (RegionStat method) cds() (Genome method) ChrLevels (class in bsxplorer) close() (SequenceFile method) (UniversalWriter method), [1] cluster() (Metagene method) (MetageneFiles method) ClusterMany (class in bsxplorer.Clusters)

ClusterPlot (class in bsxplorer.Clusters) ClusterSingle (class in bsxplorer.Clusters) colnames() (UniversalBatch class method) compare() (ClusterMany method) context_box_plot() (Metagene method) contexts_line_plot() (Metagene method) cut_tree() (ClusterMany method) (ClusterSingle method)

D

dendrogram() (MetageneFiles method) draw_mpl() (BoxPlot method) (ClusterPlot method) (HeatMap method) (LinePlot method) (PCA method)

draw_plotly() (BoxPlot method) (ClusterPlot method) (HeatMap method) (LinePlot method) (PCA method)

E

enrich() (Enrichment method) Enrichment (class in bsxplorer)

EnrichmentResult (class in bsxplorer) epipolymorphism() (PivotRegion method), [1] exon() (Genome method)

F

file_size (UniversalReader property) filter() (ChrLevels method) (Metagene method) (MetageneFiles method) (PivotRegion method) (RegionStat method) filter_data() (UniversalBatch method), [1] filter_not_none() (UniversalBatch method), [1] from_bedGraph() (ChrLevels class method) (Metagene class method) from_binom() (ChrLevels class method) (Metagene class method) from_bismark() (ChrLevels class method) (Metagene class method)

from_calls() (PivotRegion class method) from_cgmap() (ChrLevels class method) (Metagene class method) from_coverage() (ChrLevels class method) (Metagene class method) from_csv() (RegionStat class method) from_custom() (Genome class method) from_expanded() (RegionStat class method) from_gff() (Genome class method) from_list() (MetageneFiles class method) from_report() (BinomialData class method) full_size (UniversalReplicatesReader property)

G

gene_body() (Genome method) Genome (class in bsxplorer)

get_module_ids() (ClusterPlot method) get_validated() (UniversalBatch method)

H

heat_map() (Metagene method) (MetageneFiles method)

HeatMap (class in bsxplorer)

K

kmeans() (ClusterMany method) (ClusterSingle method)

L

line_plot() (ChrLevels method) (Metagene method) (MetageneFiles method)

LinePlot (class in bsxplorer)

M

matrix_df() (PivotRegion method) merge() (MetageneFiles method) Metagene (class in bsxplorer) metagene_coverage() (EnrichmentResult method)

MetageneFiles (class in bsxplorer) methylation_entropy() (PivotRegion method), [1] module_corr() (ClusterPlot method) mpl_box_data() (BoxPlot method)

N

near_TES() (Genome method)

near_TSS() (Genome method)

O

open() (UniversalWriter method), [1]

other() (Genome method)

P

pa_schema() (UniversalBatch class method) PCA (class in bsxplorer) PDR() (PivotRegion method), [1] PivotRegion (class in bsxplorer)

pl_schema() (UniversalBatch class method), [1] plot_density_mpl() (EnrichmentResult method) plot_enrich_mpl() (EnrichmentResult method) plot_qc() (BAMReader method), [1] preprocess_cytosines() (SequenceFile method)

Q

qc_data() (BAMReader method), [1]

R

raw() (Genome method) read_total_stats() (BinomialData class method) ref_positions() (EnrichmentResult method) region_pvalue() (BinomialData method)

RegionStat (class in bsxplorer) report_iter() (BAMReader method), [1] resize() (Metagene method) (MetageneFiles method)

S

save() (RegionStat method) save_plot_rds() (ChrLevels method)

save_tsv() (ClusterPlot method) SequenceFile (class in bsxplorer) stats_iter() (BAMReader method), [1]

T

to_arrow() (UniversalBatch method) to_bedGraph() (UniversalBatch method), [1] to_bismark() (UniversalBatch method), [1]

to_cgmap() (UniversalBatch method), [1] to_coverage() (UniversalBatch method), [1] trim_flank() (Metagene method) (MetageneFiles method)

U

UniversalBatch (class in bsxplorer) UniversalReader (class in bsxplorer)

UniversalReplicatesReader (class in bsxplorer) UniversalWriter (class in bsxplorer)

V

validate() (Genome class method)

W

write() (UniversalWriter method), [1]