Index

_

_create_heatmap() (in module pyllelic.visualization) _create_histogram() (in module pyllelic.visualization) _create_methylation_diffs_bar_graph() (in module pyllelic.visualization) _make_binary() (in module pyllelic.visualization)

_make_methyl_df() (in module pyllelic.visualization) _make_stacked_fig() (in module pyllelic.visualization) _make_stacked_mpl_fig() (in module pyllelic.visualization) _make_stacked_plotly_fig() (in module pyllelic.visualization)

A

AD_stats (class in pyllelic.pyllelic) aliLen (pyllelic.quma.Result attribute)

aliMis (pyllelic.quma.Result attribute) allelic_data (pyllelic.pyllelic.GenomicPositionData attribute) analysis_directory (pyllelic.config.Config attribute)

B

BamOutput (class in pyllelic.pyllelic) base_directory (pyllelic.config.Config attribute)

bismark() (in module pyllelic.process) bowtie2_fastq_to_bam() (in module pyllelic.process) build_bowtie2_index() (in module pyllelic.process)

C

cell_types (pyllelic.pyllelic.GenomicPositionData attribute) chromosome (pyllelic.config.Config attribute) com (pyllelic.quma.Fasta attribute) Config (class in pyllelic.config)

config (pyllelic.pyllelic.GenomicPositionData attribute) configure() (in module pyllelic.pyllelic) conv (pyllelic.quma.Result attribute) convert_methbank_bed() (in module pyllelic.process) crits (pyllelic.pyllelic.AD_stats attribute)

D

data (pyllelic.quma.Quma attribute)

diffs (pyllelic.pyllelic.GenomicPositionData attribute) dir (pyllelic.quma.Reference attribute)

E

exc (pyllelic.quma.Reference attribute)

F

Fasta (class in pyllelic.quma) fasta (pyllelic.quma.Reference attribute) fastq_to_list() (in module pyllelic.process) file_names (pyllelic.pyllelic.GenomicPositionData attribute)

FileNameError files_set (pyllelic.pyllelic.GenomicPositionData attribute) fname_pattern (pyllelic.config.Config attribute) from_pickle() (pyllelic.pyllelic.GenomicPositionData static method)

G

gAli (pyllelic.quma.Result attribute) gap (pyllelic.quma.Result attribute) gdir (pyllelic.quma.Reference attribute)

generate_ad_stats() (pyllelic.pyllelic.GenomicPositionData method) genome_values (pyllelic.pyllelic.BamOutput attribute) GenomicPositionData (class in pyllelic.pyllelic)

H

heatmap() (pyllelic.pyllelic.GenomicPositionData method)

histogram() (pyllelic.pyllelic.GenomicPositionData method)

I

index_bam() (in module pyllelic.process)

individual_data (pyllelic.pyllelic.GenomicPositionData attribute)

M

make_list_of_bam_files() (in module pyllelic.pyllelic) make_records_to_dictionary() (in module pyllelic.process) match (pyllelic.quma.Result attribute) means (pyllelic.pyllelic.GenomicPositionData attribute) menum (pyllelic.quma.Result attribute) modes (pyllelic.pyllelic.GenomicPositionData attribute)

module pyllelic.__main__ pyllelic.config pyllelic.process pyllelic.pyllelic pyllelic.quma pyllelic.visualization

N

name (pyllelic.pyllelic.BamOutput attribute)

O

offset (pyllelic.config.Config attribute)

P

pconv (pyllelic.quma.Result attribute) perc (pyllelic.quma.Result attribute) pos (pyllelic.quma.Fasta attribute) positions (pyllelic.pyllelic.BamOutput attribute) (pyllelic.pyllelic.GenomicPositionData attribute) prepare_genome() (in module pyllelic.process) promoter_end (pyllelic.config.Config attribute) promoter_file (pyllelic.config.Config attribute) promoter_start (pyllelic.config.Config attribute) pyllelic() (in module pyllelic.pyllelic) pyllelic.__main__ module

pyllelic.config module pyllelic.process module pyllelic.pyllelic module pyllelic.quma module pyllelic.visualization module

Q

qAli (pyllelic.quma.Result attribute) Quma (class in pyllelic.quma)

quma_output (pyllelic.pyllelic.QumaResult attribute) quma_results (pyllelic.pyllelic.GenomicPositionData attribute) QumaResult (class in pyllelic.pyllelic)

R

reads_graph() (pyllelic.pyllelic.GenomicPositionData method) Reference (class in pyllelic.quma) res (pyllelic.quma.Reference attribute)

Result (class in pyllelic.quma) results_directory (pyllelic.config.Config attribute) retrieve_seq() (in module pyllelic.process) run_pyllelic() (in module pyllelic.__main__)

S

save() (pyllelic.pyllelic.GenomicPositionData method) save_pickle() (pyllelic.pyllelic.GenomicPositionData method) seq (pyllelic.quma.Fasta attribute) ShellCommandError

sig (pyllelic.pyllelic.AD_stats attribute) sig_methylation_differences() (pyllelic.pyllelic.GenomicPositionData method) sort_bam() (in module pyllelic.process) stat (pyllelic.pyllelic.AD_stats attribute) summarize_allelic_data() (pyllelic.pyllelic.GenomicPositionData method)

U

unconv (pyllelic.quma.Result attribute)

V

val (pyllelic.quma.Result attribute) values (pyllelic.pyllelic.BamOutput attribute) (pyllelic.pyllelic.QumaResult attribute) (pyllelic.quma.Quma attribute)

viz_backend (pyllelic.config.Config attribute)

W

write_means_modes_diffs() (pyllelic.pyllelic.GenomicPositionData method)