diff --git a/README.md b/README.md
index efde9358..f417fd24 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@
 [![codecov](https://codecov.io/gh/poldracklab/nitransforms/branch/master/graph/badge.svg)](https://codecov.io/gh/poldracklab/nitransforms)
 [![doi](https://img.shields.io/badge/doi-10.31219%2Fosf.io%2F8aq7b-blue.svg)](https://doi.org/10.31219/osf.io/8aq7b)
 [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/poldracklab/nitransforms/master?filepath=docs%2Fnotebooks%2F)
+[![Docs](https://readthedocs.org/projects/nitransforms/badge/?version=latest)](http://nitransforms.readthedocs.io/en/latest/?badge=latest)
 
 A development repo for [nipy/nibabel#656](https://github.com/nipy/nibabel/pull/656)
 
@@ -23,6 +24,6 @@ to apply transforms generated by the most popular neuroimaging packages and libr
 (AFNI, FSL, FreeSurfer, ITK, and SPM).
 The proposed software is subject to continuous integration tests to check the
 compatibility with each supported tool after every change to the code base.
-Compatibility between software tools and imaging formats is a necessary bridge 
+Compatibility between software tools and imaging formats is a necessary bridge
 to ensure the reproducibility of results and enable the optimization and evaluation
 of current image processing and analysis workflows.
diff --git a/docs/_api/base.rst b/docs/_api/base.rst
new file mode 100644
index 00000000..56482d9a
--- /dev/null
+++ b/docs/_api/base.rst
@@ -0,0 +1,6 @@
+====
+Base
+====
+
+.. automodule:: nitransforms.base
+    :members:
diff --git a/docs/_api/io.rst b/docs/_api/io.rst
new file mode 100644
index 00000000..7666253b
--- /dev/null
+++ b/docs/_api/io.rst
@@ -0,0 +1,39 @@
+===
+IO
+===
+
+Reading and writing of transform files.
+
+--------
+Base I/O
+--------
+.. automodule:: nitransforms.io.base
+    :members:
+
+-----------------
+Tool Specific I/O
+-----------------
+
+^^^^
+AFNI
+^^^^
+.. automodule:: nitransforms.io.afni
+    :members:
+
+^^^
+FSL
+^^^
+.. automodule:: nitransforms.io.fsl
+    :members:
+
+^^^
+ITK
+^^^
+.. automodule:: nitransforms.io.itk
+    :members:
+
+^^^^^^^^^^^^^^
+FreeSurfer/LTA
+^^^^^^^^^^^^^^
+.. automodule:: nitransforms.io.lta
+    :members:
diff --git a/docs/_api/linear.rst b/docs/_api/linear.rst
new file mode 100644
index 00000000..728b2ed0
--- /dev/null
+++ b/docs/_api/linear.rst
@@ -0,0 +1,6 @@
+=================
+Linear Transforms
+=================
+
+.. automodule:: nitransforms.linear
+    :members:
diff --git a/docs/_api/manip.rst b/docs/_api/manip.rst
new file mode 100644
index 00000000..b14f1fd3
--- /dev/null
+++ b/docs/_api/manip.rst
@@ -0,0 +1,6 @@
+=============
+Manipulations
+=============
+
+.. automodule:: nitransforms.manip
+    :members:
diff --git a/docs/_api/nonlinear.rst b/docs/_api/nonlinear.rst
new file mode 100644
index 00000000..ab3574b4
--- /dev/null
+++ b/docs/_api/nonlinear.rst
@@ -0,0 +1,6 @@
+====================
+Nonlinear Transforms
+====================
+
+.. automodule:: nitransforms.nonlinear
+    :members:
diff --git a/docs/_api/patched.rst b/docs/_api/patched.rst
new file mode 100644
index 00000000..b50cb6de
--- /dev/null
+++ b/docs/_api/patched.rst
@@ -0,0 +1,6 @@
+=========================
+Patched Nibabel Functions
+=========================
+
+.. automodule:: nitransforms.patched
+    :members:
diff --git a/docs/api.rst b/docs/api.rst
index 1d87ebd2..2d67b21b 100644
--- a/docs/api.rst
+++ b/docs/api.rst
@@ -3,12 +3,11 @@ Library API (application program interface)
 Information on specific functions, classes, and methods for developers.
 
 .. toctree::
-   :glob:
+   :maxdepth: 1
 
-   api/nitransforms.base
-   api/nitransforms.cli
-   api/nitransforms.io
-   api/nitransforms.linear
-   api/nitransforms.manip
-   api/nitransforms.nonlinear
-   api/nitransforms.patched
\ No newline at end of file
+   _api/base
+   _api/io
+   _api/linear
+   _api/manip
+   _api/nonlinear
+   _api/patched