From 11bd32fd4adb5ba1238f44d5550bedf0c4fdc9a0 Mon Sep 17 00:00:00 2001 From: maikia Date: Thu, 5 Jan 2023 14:35:25 +0100 Subject: [PATCH] rearanging things --- docs/source/index.rst | 66 ++++++--------------------- docs/source/usage/contributing.rst | 5 ++ docs/source/usage/getting_started.rst | 11 +++++ docs/source/usage/installation.rst | 20 ++++++++ docs/source/usage/requirements.rst | 13 ++++++ 5 files changed, 62 insertions(+), 53 deletions(-) create mode 100644 docs/source/usage/contributing.rst create mode 100644 docs/source/usage/getting_started.rst create mode 100644 docs/source/usage/installation.rst create mode 100644 docs/source/usage/requirements.rst diff --git a/docs/source/index.rst b/docs/source/index.rst index 87dd9597..b5ecb2e3 100644 --- a/docs/source/index.rst +++ b/docs/source/index.rst @@ -3,8 +3,8 @@ You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. -Welcome to PyDESeq2's documentation! -==================================== +PyDESeq2 documentation +====================== This package is a python implementation of the `DESeq2 `_ method [1]_ for differential expression analysis (DEA) with bulk RNA-seq data, originally in R. @@ -15,73 +15,33 @@ As PyDESeq2 is a re-implementation of `DESeq2 `_ LFC shrinkage [2]_. We plan to implement more in the near future. In case there is a feature you would particularly like to be implemented, feel free to open an issue on GitHub. + .. toctree:: :maxdepth: 2 - :caption: Contents: - - api/index - -Installation ------------- - -`PyDESeq2` can be installed from PyPI: - -.. code-block:: bash - - pip install pydeseq2 - -We recommend installing within a conda environment: - -.. code-block:: python - - conda env create -n pydeseq2 - conda activate pydeseq2 - pip install pydeseq2 - - -If you're interested in contributing or want access to the development version, please see the :ref:`contributing`. + :caption: Usage: -Requirements ------------- + usage/installation + usage/requirements + usage/getting_started + usage/contributing -The list of package version requirements is available in ``setup.py``, and will be automatically installed along PyDESeq2 when using PyPI. -For reference, the code was tested with python 3.8 and the following package versions: +.. toctree:: + :maxdepth: 2 + :caption: Contents: -- numpy 1.23.0 -- pandas 1.4.3 -- scikit-learn 1.1.1 -- scipy 1.8.1 -- statsmodels 0.13.2 + api/index -Please don't hesitate to open an issue in case you encounter any issue due to possible deprecations. Documentation ------------- The documentation is automatically build using `Sphinx `_, and hosted `here on ReadTheDoc `_. -Getting started ---------------- - -The `notebooks directory `_ contains minimal examples on how to use PyDESeq2, in the form of jupyter notebooks. - -You can also try them from your browser (on synthetic data only): |Binder| - -.. |Binder| image:: https://mybinder.org/badge_logo.svg - :target: https://mybinder.org/v2/gh/owkin/PyDESeq2/HEAD?labpath=notebooks%2Findex.ipynb - -.. _contributing: - -Contributing ------------- - -PyDESeq2 is a living project and any contributions are welcome! The project is hosted on `Github `_. -Feel free to come and open new PRs or issues. Citing this work ---------------- -:: +:: @article{muzellec2022pydeseq2, title={PyDESeq2: a python package for bulk RNA-seq differential expression analysis}, diff --git a/docs/source/usage/contributing.rst b/docs/source/usage/contributing.rst new file mode 100644 index 00000000..2a8451d6 --- /dev/null +++ b/docs/source/usage/contributing.rst @@ -0,0 +1,5 @@ +Contributing +------------ + +PyDESeq2 is a living project and any contributions are welcome! The project is hosted on `Github `_. +Feel free to come and open new PRs or issues. \ No newline at end of file diff --git a/docs/source/usage/getting_started.rst b/docs/source/usage/getting_started.rst new file mode 100644 index 00000000..c42c74ae --- /dev/null +++ b/docs/source/usage/getting_started.rst @@ -0,0 +1,11 @@ +Getting started +--------------- + +The `notebooks directory `_ contains minimal examples on how to use PyDESeq2, in the form of jupyter notebooks. + +You can also try them from your browser (on synthetic data only): |Binder| + +.. |Binder| image:: https://mybinder.org/badge_logo.svg + :target: https://mybinder.org/v2/gh/owkin/PyDESeq2/HEAD?labpath=notebooks%2Findex.ipynb + +.. _contributing: \ No newline at end of file diff --git a/docs/source/usage/installation.rst b/docs/source/usage/installation.rst new file mode 100644 index 00000000..05c8c898 --- /dev/null +++ b/docs/source/usage/installation.rst @@ -0,0 +1,20 @@ +Installation +------------ + +`PyDESeq2` can be installed from PyPI: + +.. code-block:: bash + + pip install pydeseq2 + +We recommend installing within a conda environment: + +.. code-block:: python + + conda env create -n pydeseq2 + conda activate pydeseq2 + pip install pydeseq2 + + +If you're interested in contributing or want access to the development version, +please see the :doc:`contributing`. \ No newline at end of file diff --git a/docs/source/usage/requirements.rst b/docs/source/usage/requirements.rst new file mode 100644 index 00000000..68a759b7 --- /dev/null +++ b/docs/source/usage/requirements.rst @@ -0,0 +1,13 @@ +Requirements +------------ + +The list of package version requirements is available in ``setup.py``, and will be automatically installed along PyDESeq2 when using PyPI. +For reference, the code was tested with python 3.8 and the following package versions: + +- numpy 1.23.0 +- pandas 1.4.3 +- scikit-learn 1.1.1 +- scipy 1.8.1 +- statsmodels 0.13.2 + +Please don't hesitate to open an issue in case you encounter any problems due to possible deprecations. \ No newline at end of file