janggu.data - Genomics datasets for deep learning

=========================================================

.. currentmodule:: janggu.data

.. autosummary::

   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

---------------------

.. autosummary::

   Dataset

   Cover

   Bioseq

   Array

   GenomicIndexer

.. autoclass:: Dataset

   :members: name, shape

.. autoclass:: Cover

   :members: create_from_bam, create_from_bigwig, create_from_bed, create_from_array

.. autoclass:: Bioseq

   :members: create_from_refgenome, create_from_seq

.. autoclass:: Array

.. autoclass:: GenomicIndexer

   :members: create_from_file

Dataset wrappers

----------------

Utilities for reshaping, data augmentation, NaN removal.

.. autosummary::

   ReduceDim

   SqueezeDim

   Transpose

   NanToNumConverter

   RandomOrientation

   RandomSignalScale

.. autoclass:: ReduceDim

.. autoclass:: SqueezeDim

.. autoclass:: Transpose

.. autoclass:: NanToNumConverter

.. autoclass:: RandomOrientation

.. autoclass:: RandomSignalScale

.. autoclass:: RandomShift

Normalization and transformation

--------------------------------

.. autosummary::

   LogTransform

   PercentileTrimming

   RegionLengthNormalization

   ZScore

   ZScoreLog

   normalize_garray_tpm

.. autoclass:: LogTransform

.. autoclass:: PercentileTrimming

.. autoclass:: RegionLengthNormalization

.. autoclass:: ZScore

.. autoclass:: ZScoreLog

.. autofunction:: normalize_garray_tpm

Visualization utilitites

------------------------

.. autofunction:: plotGenomeTrack

.. autoclass:: Track

.. autoclass:: HeatTrack

.. autoclass:: LineTrack

.. autoclass:: SeqTrack