Merge pull request #98 from theislab/dev

Dev

Author: davidsebfischer

README.md

@@ -0,0 +1,22 @@
+|PyPI| |Docs|
+
+.. |PyPI| image:: https://img.shields.io/pypi/v/diffxpy.svg
+   :target: https://pypi.org/project/diffxpy
+.. |Docs| image:: https://readthedocs.com/projects/diffxpy/badge/?version=latest
+   :target: https://diffxpy.readthedocs.io
+
+Fast and scalable differential expression analysis on single-cell RNA-seq data
+==============================================================================
+
+diffxpy covers a wide range of differential expression analysis scenarios encountered in single-cell RNA-seq scenarios
+and integrates into scanpy_ workflows.
+Import diffxpy as `import diffxpy.api as de` to access the following differential expression analysis-related tools:
+
+1. **differential expression analysis** in the module `de.test.*`
+2. **gene set enrichment analysis** based on differential expression calls in the module  `de.enrich.*`
+
+Refer to the documentation_ and the tutorials_ for details of these modules.
+
+.. _scanpy: https://github.com/theislab/scanpy
+.. _documentation: https://diffxpy.rtfd.io/en/latest
+.. _tutorials: https://diffxpy.rtfd.io/en/latest/tutorials.html

README.rst

@@ -5,7 +5,7 @@
 author_email='david.fischer@helmholtz-muenchen.de, diffxpy@frhoelzlwimmer.de'
 description="Fast and scalable differential expression analysis on single-cell RNA-seq data"
 
-with open("README.md", "r") as fh:
+with open("README.rst", "r") as fh:
      long_description = fh.read()
 
 setup(
@@ -21,7 +21,7 @@
         'scipy',
         'pandas',
         'patsy>=0.5.0',
-        'batchglm>=0.6.0',
+        'batchglm>=0.6.1',
         'xarray',
         'statsmodels',
     ],