finished rtfd documentation and resturctured examples.

Author: davidsebfischer

docs/_static/css/custom.css

@@ -10,11 +10,10 @@ Welcome to diffxpy's documentation!
    :maxdepth: 2
    :caption: Contents:
 
+   installation
+   tutorials
    api/index
-   examples
-..   basic_usage
-..   installation
-..   references
+   references
 
 
 Indices and tables

docs/examples.rst

@@ -0,0 +1,43 @@
+Installation
+============
+
+We assume that you have a python environment set up.
+
+Firstly, you need to install batchglm which depdends on the PyPi packages and tensorflow and tensorflow-probability.
+You can install these dependencies from source to optimze them to your hardware which can improve performance.
+Note that both packages also have GPU versions which allows you to run the run-time limiting steps of diffxpy on GPUs.
+The simplest installation of these dependencies is via pip: call::
+
+    pip install tf-nightly
+    pip install tfp-nightly
+
+The nightly versions of tensorflow and tensorflow-probability are up-to-date versions of these packages.
+Alternatively you can also install the major releases: call::
+
+    pip install tensorflow
+    pip install tensorflow-probability
+
+
+You can then install batchglm from source by using the repository on `GitHub
+<https://github.com/theislab/batchglm>`__: 
+
+- Chose a directory where you want batchglm to be located and ``cd`` into it.
+- Clone the batchglm repository into this directory.
+- ``cd`` into the root directory of batchglm.
+- Install batchglm from source: call::
+
+    pip install -e .
+
+Finally, you can then install diffxpy from source by using the repository on `GitHub
+<https://github.com/theislab/diffxpy>`__: 
+
+- Chose a directory where you want batchglm to be located and ``cd`` into it.
+- Clone the diffxpy repository into this directory.
+- ``cd`` into the root directory of diffxpy.
+- Install diffxpy from source: call::
+
+    pip install -e .
+
+You can now use diffxpy in a python session by via the following import: call::
+
+    import diffxpy.api as de 

docs/index.rst

@@ -0,0 +1,2 @@
+References
+==========

docs/installation.rst

@@ -0,0 +1,53 @@
+Tutorials
+=========
+
+
+------------
+
+Differential testing
+--------------------
+
+Single tests per gene
+~~~~~~~~~~~~~~~~~~~~~
+
+How to perform likelihood-ratio tests `lrt <https://github.com/theislab/diffxpy/tutorials/test/single/likelihood_ratio_test.ipynb>`__.
+
+How to perform Wald tests `wald <https://github.com/theislab/diffxpy/tutorials/test/single/wald_test.ipynb>`__.
+
+How to perform t-tests `t_test <https://github.com/theislab/diffxpy/tutorials/test/single/t_test.ipynb>`__.
+
+How to perform Wilcoxon tests `wilcoxon <https://github.com/theislab/diffxpy/tutorials/test/single/wilcoxon_test.ipynb>`__.
+
+Map single tests across partitions of data set
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Set up a test and conduct test for each gene in each cluster or each sample etc.
+We show an example for doing this for a t-test in `partition <https://github.com/theislab/diffxpy/tutorials/test/single/run_by_partition.ipynb>`__.
+   
+Multiple tests per gene
+~~~~~~~~~~~~~~~~~~~~~~~
+
+How to perform pairwise tests `pairwise <https://github.com/theislab/diffxpy/tutorials/test/multi/pairwise.ipynb>`__.
+
+How to perform group versus rest tests `versus_rest <https://github.com/theislab/diffxpy/tutorials/test/multiversus_rest.ipynb>`__.
+
+
+Gene set enrichment: enrich
+---------------------------
+
+How to conduct a gene set enrichment workflow `enrich <https://github.com/theislab/diffxpy/tutorials/enrich/enrich.ipynb>`__.
+
+
+Integration with other packages
+-------------------------------
+
+How to integrate with `scanpy <https://github.com/theislab/diffxpy/tutorials/integration/scanpy_integration.ipynb>`__.
+
+
+Example work-flows on real data sets
+------------------------------------
+
+HCA immune cell `atlas <https://github.com/theislab/diffxpy/tutorials/real_data/ImmuneCellAtlas.ipynb>`__.
+
+Mouse brain `atlas <https://github.com/theislab/diffxpy/tutorials/real_data/MouseBrainCellAtlas.ipynb>`__.
+