Metadata-Version: 2.1
Name: anutils
Version: 0.4.1
Summary: ml and single cell utils.
Home-page: https://github.com/AaronNing/anutils
Author: Aaron Ning
Author-email: aaronning98@gmail.com
License: MIT
Keywords: anutils

anutils
=======

ML and single cell analysis utils.

installation
------------

::

   pip install anutils

**NOTE**: To use ``anutils.scutils.sc_cuda``, you need to install rapids
first. see `rapids.ai <https://rapids.ai/start.html>`__ for details. For
example, to install rapids on a linux machine with cuda 11, you can run:

.. code:: bash

   pip install cudf-cu11 dask-cudf-cu11 --extra-index-url=https://pypi.nvidia.com
   pip install cuml-cu11 --extra-index-url=https://pypi.nvidia.com
   pip install cugraph-cu11 --extra-index-url=https://pypi.nvidia.com

usage
-----

general utils: ``anutils.*``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~

e.g., reload module

.. code:: python

   import sys
   sys.path.append('/path/to/some/packaege/')
   import some_package

   # change some_package.sub_module.func, recursive reload needed
   from anutils import rreload
   rreload(some_package, max_depth=2)

single cell utils: ``anutils.scutils.*``
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

plotting
^^^^^^^^

.. code:: python

   from anutils import scutils as scu

   # a series of embeddings grouped by disease status
   scu.pl.embeddings(adata, basis='X_umap', groupby='disease_status', **kwargs) # kwargs for sc.pl.embedding

   # enhanced dotplot with groups in hierarchical order
   scu.pl.dotplot(adata, var_names, groupby, **kwargs) # kwargs for sc.pl.dotplot

cuda-accelerated scanpy functions
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

NOTE: to use these functions, you need to install rapids first. see
`installation <#installation>`__ for details.

.. code:: python

   from anutils.scutils import sc_cuda as cusc

   # 10-100 times faster than `scanpy.tl.leiden`
   cusc.sc.leiden(adata, resolution=0.5, key_added='leiden_0.5')

   # 10-100 times faster than `scib.metrics.silhouette`
   cusc.sb.silhouette(adata, group_key, embed)

machine learning utils:
-----------------------

.. code:: python

   import anutils.mlutils as ml

   # to be added
