janggu.data.rst

janggu.data - Genomics datasets for deep learning

janggu.data

Bioseq.create_from_seq Bioseq.create_from_refgenome Cover.create_from_bam Cover.create_from_bigwig Cover.create_from_bed Cover.create_from_array plotGenomeTrack Track HeatTrack LineTrack SeqTrack

Main Dataset classes

Dataset Cover Bioseq Array GenomicIndexer

Dataset

Cover

Bioseq

Array

GenomicIndexer

Dataset wrappers

Utilities for reshaping, data augmentation, NaN removal.

ReduceDim NanToNumConverter RandomOrientation RandomSignalScale

ReduceDim

NanToNumConverter

RandomOrientation

RandomSignalScale

Normalization and transformation

LogTransform PercentileTrimming RegionLengthNormalization ZScore ZScoreLog normalize_garray_tpm

LogTransform

PercentileTrimming

RegionLengthNormalization

ZScore

ZScoreLog

normalize_garray_tpm

Visualization utilitites

plotGenomeTrack

Track

HeatTrack

LineTrack

SeqTrack