first new version of rtfd documentation - manual changes to .rst files

Author: davidsebfischer

docs/api/index.rst

@@ -1,25 +1,55 @@
-.. automodule:: diffxpy
+.. automodule:: diffxpy.api
 
 API
 ===
 
-
 Import diffxpy's high-level API as::
 
-   import diffxpy as de
+   import diffxpy.api as de
+
+Differential expression tests: test
+-----------------------------------
+
+Run differential expression tests.
+
+Single tests per gene
+~~~~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: .
+
+   test.two_sample
+   test.wald
+   test.lrt
+   test.t_test
+   test.wilcoxon
+
+Multiple tests per gene
+~~~~~~~~~~~~~~~~~~~~~~~
 
+.. autosummary::
+   :toctree: .
+
+   test.pairwise
+   test.versus_rest
+   test.partition
+
+
+Gene set enrichment: enrich
+---------------------------
 
-.. For visual quality control, see :func:`~scanpy.api.pl.highest_expr_gens` and
-.. :func:`~scanpy.api.pl.filter_genes_dispersion` in the :doc:`plotting API <plotting>`.
+Reference gene sets
+~~~~~~~~~~~~~~~~~~~
 
 .. autosummary::
    :toctree: .
 
-   stats
-   test_lrt
-   test_pairwise
-   test_t_test
-   test_vsrest
-   test_wald_loc
-   test_wilcoxon
+   enrich.RefSets
+
+Enrichment tests
+~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: .
 
+   enrich.test

docs/examples.rst

@@ -0,0 +1,53 @@
+.. automodule:: diffxpy.api
+
+Examples
+========
+
+Import diffxpy's high-level API as::
+
+   import diffxpy.api as de
+
+Differential expression tests: test
+-----------------------------------
+
+Run differential expression tests.
+
+Single tests per gene
+~~~~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: .
+
+   single/likelihood_ratio_test.ipynb
+   single/run_by_partition.ipynb
+   single/t_test.ipynb
+   single/test_chisq_distribution.ipynb
+   single/wald_test.ipynb
+   single/wilcoxon_test.ipynb
+   
+Multiple tests per gene
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. autosummary::
+   :toctree: .
+
+   versus_rest.ipynb
+   pairwise.ipynb
+
+
+Gene set enrichment: enrich
+---------------------------
+
+.. autosummary::
+   :toctree: .
+
+   enrich.ipynb
+
+
+Integration with other packages
+-------------------------------
+
+.. autosummary::
+   :toctree: .
+
+   scanpy_integration.ipynb

docs/index.rst

@@ -1,7 +1,5 @@
-.. batchglm documentation master file, created by
-    sphinx-quickstart on Mon Jul 30 15:55:16 2018.
-    You can adapt this file completely to your liking, but it should at least
-    contain the root `toctree` directive.
+.. You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
 
 
 
@@ -13,7 +11,7 @@ Welcome to diffxpy's documentation!
    :caption: Contents:
 
    api/index
-..   examples
+   examples
 ..   basic_usage
 ..   installation
 ..   references