diff --git a/docs/conf.py b/docs/conf.py
index 3575773..7254626 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -29,7 +29,7 @@
 # The full version, including alpha/beta/rc tags
 release = info["Version"]
 
-bibtex_bibfiles = ["references.bib"]
+# bibtex_bibfiles = ["references.bib"]
 templates_path = ["_templates"]
 nitpicky = True  # Warn about broken links
 needs_sphinx = "4.0"
@@ -53,7 +53,7 @@
     "sphinx.ext.intersphinx",
     "sphinx.ext.autosummary",
     "sphinx.ext.napoleon",
-    "sphinxcontrib.bibtex",
+    # "sphinxcontrib.bibtex",
     "sphinx_autodoc_typehints",
     "sphinx.ext.mathjax",
     "IPython.sphinxext.ipython_console_highlighting",
diff --git a/docs/contributing.md b/docs/contributing.md
index 199d352..e2fceb6 100644
--- a/docs/contributing.md
+++ b/docs/contributing.md
@@ -127,7 +127,7 @@ This project uses [sphinx][] with the following features:
 -   The [myst][] extension allows to write documentation in markdown/Markedly Structured Text
 -   [Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
 -   [sphinx-autodoc-typehints][], to automatically reference annotated input and output types
--   Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
+-   Citations can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
 
 See scanpy’s {doc}`scanpy:dev/documentation` for more information on how to write your own.
 
diff --git a/docs/api.md b/docs/dso_python.md
similarity index 84%
rename from docs/api.md
rename to docs/dso_python.md
index 7edc4c4..10cafdc 100644
--- a/docs/api.md
+++ b/docs/dso_python.md
@@ -1,4 +1,6 @@
-# API
+# Python API
+
+TODO
 
 ```{eval-rst}
 .. module:: dso
diff --git a/docs/dso_r.md b/docs/dso_r.md
new file mode 100644
index 0000000..84d5a1d
--- /dev/null
+++ b/docs/dso_r.md
@@ -0,0 +1,3 @@
+# DSO R package
+
+TODO
diff --git a/docs/getting_started.md b/docs/getting_started.md
new file mode 100644
index 0000000..c4c9314
--- /dev/null
+++ b/docs/getting_started.md
@@ -0,0 +1,3 @@
+# Getting started
+
+TODO
diff --git a/docs/index.md b/docs/index.md
index 9a736b3..01e1eec 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -5,9 +5,32 @@
 ```{toctree}
 :hidden: true
 :maxdepth: 1
+:caption: User Guide
+
+getting_started.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO CLI
 
-api.md
 CHANGELOG.md
 contributing.md
-references.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO Python API
+
+dso_python.md
+```
+
+```{toctree}
+:hidden: true
+:maxdepth: 1
+:caption: DSO R API
+
+dso_r.md
 ```
diff --git a/docs/references.bib b/docs/references.bib
deleted file mode 100644
index 9f5bed4..0000000
--- a/docs/references.bib
+++ /dev/null
@@ -1,10 +0,0 @@
-@article{Virshup_2023,
-	doi = {10.1038/s41587-023-01733-8},
-	url = {https://doi.org/10.1038%2Fs41587-023-01733-8},
-	year = 2023,
-	month = {apr},
-	publisher = {Springer Science and Business Media {LLC}},
-	author = {Isaac Virshup and Danila Bredikhin and Lukas Heumos and Giovanni Palla and Gregor Sturm and Adam Gayoso and Ilia Kats and Mikaela Koutrouli and Philipp Angerer and Volker Bergen and Pierre Boyeau and Maren Büttner and Gokcen Eraslan and David Fischer and Max Frank and Justin Hong and Michal Klein and Marius Lange and Romain Lopez and Mohammad Lotfollahi and Malte D. Luecken and Fidel Ramirez and Jeffrey Regier and Sergei Rybakov and Anna C. Schaar and Valeh Valiollah Pour Amiri and Philipp Weiler and Galen Xing and Bonnie Berger and Dana Pe'er and Aviv Regev and Sarah A. Teichmann and Francesca Finotello and F. Alexander Wolf and Nir Yosef and Oliver Stegle and Fabian J. Theis and},
-	title = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
-	journal = {Nature Biotechnology}
-}
diff --git a/docs/references.md b/docs/references.md
deleted file mode 100644
index 00ad6a6..0000000
--- a/docs/references.md
+++ /dev/null
@@ -1,5 +0,0 @@
-# References
-
-```{bibliography}
-:cited:
-```
diff --git a/pyproject.toml b/pyproject.toml
index f8bb22f..fd779a1 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -46,6 +46,7 @@ optional-dependencies.doc = [
   # For notebooks
   "ipykernel",
   "ipython",
+  "matplotlib",
   "myst-nb>=1.1",
   "sphinx>=4",
   "sphinx-autodoc-typehints",