Index

A

Aberration (class in biallelic.models) Aberrations (class in biallelic.bi) AberrationType (class in biallelic.models) About

add_log() (biallelic.logging.SimpleLogger method) AMP (biallelic.models.AberrationType attribute) API Reference Architecture

B

biallelic.bi module biallelic.logging module

biallelic.misc module biallelic.models module biallelic_inactivations() (biallelic.bi.Aberrations method)

C

camel_case_split() (in module biallelic.misc)

CNN_LOH (biallelic.models.AberrationType attribute) color_palettes() (in module biallelic.misc)

D

DefaultHelpParser (class in biallelic.misc) Development

DoubleHit (class in biallelic.models) DoubleHitType (class in biallelic.models)

E

error() (biallelic.misc.DefaultHelpParser method)

ExtendedLogger (class in biallelic.logging)

F

Female (biallelic.models.Gender attribute)

G

GAIN (biallelic.models.AberrationType attribute) GAIN_LOH (biallelic.models.AberrationType attribute) Gender (class in biallelic.models) generate_uid() (in module biallelic.misc) Genomics (biallelic.models.OmicsType attribute) GERM_HET_LOSS (biallelic.models.AberrationType attribute) GERM_HOM_LOSS (biallelic.models.AberrationType attribute) GERM_HOM_SNV (biallelic.models.AberrationType attribute) GERM_SNV (biallelic.models.AberrationType attribute)

GermLoss_GermLoss (biallelic.models.DoubleHitType attribute) GermLoss_GermSnp (biallelic.models.DoubleHitType attribute) GermLoss_GermSv (biallelic.models.DoubleHitType attribute) GermLoss_SomLoss (biallelic.models.DoubleHitType attribute) GermSnp_GermSnp (biallelic.models.DoubleHitType attribute) GermSnp_SomLoss (biallelic.models.DoubleHitType attribute) GermSv_SomLoss (biallelic.models.DoubleHitType attribute) Get started get_module_method() (in module biallelic.misc) get_modules_names() (in module biallelic.misc)

H

HET_LOSS (biallelic.models.AberrationType attribute)

HOM_LOSS (biallelic.models.AberrationType attribute)

I

import_module() (in module biallelic.misc)

INDEL (biallelic.models.AberrationType attribute)

L

load_aberration() (biallelic.bi.Aberrations method)

load_contents() (biallelic.bi.Aberrations method) load_refs() (biallelic.bi.Aberrations method)

M

make_ucsc_format() (in module biallelic.misc) Male (biallelic.models.Gender attribute) Manifest METHYL (biallelic.models.AberrationType attribute) Methylomics (biallelic.models.OmicsType attribute)

module biallelic.bi biallelic.logging biallelic.misc biallelic.models

O

OmicsType (class in biallelic.models)

P

package_modules() (in module biallelic.misc)

S

SampleDonor (class in biallelic.models) SimpleLogger (class in biallelic.logging) SNV (biallelic.models.AberrationType attribute) SomCnLoh_SomSnv (biallelic.models.DoubleHitType attribute) SomGainLoh_SomSnv (biallelic.models.DoubleHitType attribute) SomLoss_Methyl (biallelic.models.DoubleHitType attribute) SomLoss_SomIndel (biallelic.models.DoubleHitType attribute)

SomLoss_SomLoss (biallelic.models.DoubleHitType attribute) SomLoss_SomSnv (biallelic.models.DoubleHitType attribute) SomLoss_SomSv (biallelic.models.DoubleHitType attribute) SomLoss_SubclonalSnv (biallelic.models.DoubleHitType attribute) SomSnv_SomSnv (biallelic.models.DoubleHitType attribute) SubclonalLoss_SomSnv (biallelic.models.DoubleHitType attribute) SubcommandHelpFormatter (class in biallelic.misc) SV (biallelic.models.AberrationType attribute)

T

Test rRun Transcriptomics (biallelic.models.OmicsType attribute)

Troubleshooting try_import() (in module biallelic.misc)

U

Unknown (biallelic.models.Gender attribute)

X

xopen() (in module biallelic.misc)