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discern-reconstruction-0.1.1
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Wasserstein Auto-Encoder for expression reconstruction
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | discern-reconstruction-0.1.1 |
| نام | discern-reconstruction |
| نسخه کتابخانه | 0.1.1 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Fabian Hausmann |
| ایمیل نویسنده | fabian.hausmann@zmnh.uni-hamburg.de |
| آدرس صفحه اصلی | https://discern.readthedocs.io/en/latest/quickinfo.html |
| آدرس اینترنتی | https://pypi.org/project/discern-reconstruction/ |
| مجوز | MIT |
.. image:: https://github.com/imsb-uke/discern/actions/workflows/test.yml/badge.svg
:target: https://github.com/imsb-uke/discern/actions/workflows/test.yml
:alt: pipeline status
.. image:: https://readthedocs.org/projects/discern/badge/?version=latest
:target: https://discern.readthedocs.io/en/latest/?badge=latest
:alt: Documentation Status
.. image:: https://github.com/imsb-uke/discern/actions/workflows/dockerimage.yml/badge.svg
:target: https://github.com/imsb-uke/discern/actions/workflows/dockerimage.yml
:alt: Docker build status
DISCERN
=======
DISCERN is a deep learning approach to reconstruction expression information
of single-cell RNAseq data sets using a high quality reference.
Getting Started
---------------
These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.
An interactive tutorial can be found in `Tutorial.ipynb <https://github.com/imsb-uke/discern/blob/main/Tutorial.ipynb>`_.
Prerequisites
^^^^^^^^^^^^^
We use `poetry <https://python-poetry.org/>`_ for dependency management. You can get poetry by
.. code-block:: sh
pip install poetry
or (the officially recommended way)
.. code-block:: sh
curl -sSL https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py | python
Installing
^^^^^^^^^^
To get discern you can clone the repository by
.. code-block:: sh
git clone https://github.com/imsb-uke/discern.git
poetry can be used to install all further dependencies in an virtual environment.
.. code-block:: sh
cd discern
poetry install --no-dev
To finally run discern you can also directly use poetry with
.. code-block:: sh
poetry run commands
or spawn a new shell in the virtual environment
.. code-block:: sh
poetry shell
For further examples the first approach is presented.
Using discern
^^^^^^^^^^^^^
You can use the main function of discern for most use cases. Usually you have to preprocess your data by:
.. code-block:: sh
poetry run discern process <parameters.json>
An example parameters.json is provided together with an hyperparameter_search.json for hyperparameter optimization using ray[tune].
The training can be done with
.. code-block:: sh
poetry run discern train <parameters.json>
Hyperparameter optimization needs a ray server with can be started with
.. code-block:: sh
poetry run ray start --head --port 57780 --redis-password='password'
and can started with
.. code-block:: sh
poetry run discern optimize <parameters.json>
For projection 2 different modes are available:
Eval mode, which is a more general approach and can save a lot of files:
.. code-block:: sh
poetry run discern project --all_batches <parameters.json>
Or projection mode which offers a more fine grained controll to which is projected.
.. code-block:: sh
poetry run discern project --metadata="metadatacolumn:value" --metadata="metadatacolumn:" <parameters.json>
which creates to files, one is projected to the average batch calculated by a
``metadatacolumn`` and a contained ``value``.
The second file is projected to the the average for each value in "metadatacolumn"; individually.
DISCERN also supports online training. You can add new batches to your dataset after the usual ``train`` with:
.. code-block:: sh
poetry run discern onlinetraining --freeze --filename=<new_not_preprocessed_batch[es].h5ad> <parameters.json>
The data gets automatically preprocessed and added to the dataset. You can run ``project`` afterwards as usual (without the ``--filename`` flag).
``--freeze`` is important to freeze non-conditional layers in training.
Testing
^^^^^^^
For critical parts of the model several tests has been implemented. They can be run with:
.. code-block:: sh
poetry run pytest --cov=discern --cov-report=term
(Requires the development version of discern).
Some tests are slow and don't run by default, but you can run them using:
.. code-block:: sh
poetry run pytest --runslow --cov=discern --cov-report=term
Coding style
^^^^^^^^^^^^
To enforce code style guidlines `pylint <https://www.pylint.org/>`_ and `mypy <http://mypy-lang.org/>`_ are use. Example commands are shown below:
.. code-block:: sh
poetry run pylint discern ray_hyperpara.py
poetry run mypy discern ray_hyperpara.py
For automatic code formatting `yapf <https://github.com/google/yapf>`_ was used:
.. code-block:: sh
yapf -i <filename.py>
These tools are included in the dev-dependencies.
Authors
-------
* Can Ergen
* Pierre Machart
* Fabian Hausmann
نیازمندی
| مقدار | نام |
|---|---|
| >=1.6.0,<1.7.0 | ray[tune,default] |
| >=0.2.3,<0.3.0 | hyperopt |
| >=1.6.0,<2.0.0 | scanpy |
| ==2.1.0 | tensorflow |
| >=0.7.1,<0.8.0 | tensorflow-addons |
| >=0.29.16,<0.30.0 | Cython |
| >=0.23.1,<0.24.0 | scikit-learn |
| <0.35.0 | llvmlite |
| >=5.5.0,<6.0.0) | ipykernel |
| >=1.0.1,<2.0.0 | joblib |
| >=7.1.2,<8.0.0 | click |
| >=4.1.1,<5.0.0) | Sphinx |
| >=0.5.2,<0.6.0) | sphinx-rtd-theme |
| >=0.10.2,<0.11.0) | toml |
زبان مورد نیاز
| مقدار | نام |
|---|---|
| >=3.6.9,<4.0.0 | Python |
نحوه نصب
نصب پکیج whl discern-reconstruction-0.1.1:
pip install discern-reconstruction-0.1.1.whl
نصب پکیج tar.gz discern-reconstruction-0.1.1:
pip install discern-reconstruction-0.1.1.tar.gz