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cnvlib package

Module cnvlib contents

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The one function exposed at the top level, read, loads a file in CNVkit's BED-like tabular format and returns a CopyNumArray instance. For your own scripting, you can usually accomplish what you need using just the CopyNumArray and GenomicArray methods available on this returned object (see :ref:`api_classes`).

To load other file formats, see :ref:`api_tabio`. To run functions equivalent to CNVkit commands within Python, see :ref:`api_commands`.

Core classes

The core objects used throughout CNVkit. The base class is GenomicArray from :doc:`skgenome`. All of these classes wrap a pandas DataFrame instance, which is accessible through the .data attribute and can be used for any manipulations that aren't already provided by methods in the wrapper class.

cnary

.. automodule:: cnvlib.cnary
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vary

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Interface to CNVkit sub-commands

commands

The public API for each of the commands defined in the CNVkit workflow.

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The following modules implement lower-level functionality specific to each of the CNVkit sub-commands.

access

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antitarget

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autobin

.. automodule:: cnvlib.autobin
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batch

.. automodule:: cnvlib.batch
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call

.. automodule:: cnvlib.call
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coverage

.. automodule:: cnvlib.coverage
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diagram

.. automodule:: cnvlib.diagram
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export

.. automodule:: cnvlib.export
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fix

.. automodule:: cnvlib.fix
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heatmap

.. automodule:: cnvlib.heatmap
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importers

.. automodule:: cnvlib.importers
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import_rna

.. automodule:: cnvlib.import_rna
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metrics

.. automodule:: cnvlib.metrics
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reference

.. automodule:: cnvlib.reference
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reports

Supports the sub-commands :ref:`breaks` and :ref:`genemetrics`.

.. automodule:: cnvlib.reports
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scatter

.. automodule:: cnvlib.scatter
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segmentation

.. automodule:: cnvlib.segmentation
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segmetrics

.. automodule:: cnvlib.segmetrics
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target

.. automodule:: cnvlib.target
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Helper modules

cmdutil

.. automodule:: cnvlib.cmdutil
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core

.. automodule:: cnvlib.core
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descriptives

.. automodule:: cnvlib.descriptives
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parallel

.. automodule:: cnvlib.parallel
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params

Defines several constants used in the pipeline.

.. automodule:: cnvlib.params
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plots

.. automodule:: cnvlib.plots
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rna

.. automodule:: cnvlib.rna
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samutil

.. automodule:: cnvlib.samutil
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segfilters

.. automodule:: cnvlib.segfilters
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smoothing

.. automodule:: cnvlib.smoothing
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