From 1f2a0d457b00ae6fd15910b1fde6b638f6130c3a Mon Sep 17 00:00:00 2001
From: huidongchen <hd7chen@gmail.com>
Date: Mon, 18 Oct 2021 22:28:27 -0400
Subject: [PATCH] update docs

---
 docs/source/Citation.rst |  6 +++++-
 docs/source/conf.py      | 14 +++++++-------
 docs/source/index.rst    | 18 ++++++++++++++++--
 3 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/docs/source/Citation.rst b/docs/source/Citation.rst
index bcfef9e..600d29c 100755
--- a/docs/source/Citation.rst
+++ b/docs/source/Citation.rst
@@ -1,2 +1,6 @@
 Citation
-========
\ No newline at end of file
+========
+
+Chen, H., Ryu, J., Vinyard, M.E., Lerer, A. & Pinello, L. SIMBA: SIngle-cell eMBedding Along with features. bioRxiv, 2021.2010.2017.464750 (2021).
+
+Please check out our `preprint <https://www.biorxiv.org/content/10.1101/2021.10.17.464750v1>`_ on bioRxiv to learn more.
\ No newline at end of file
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 6acf532..bfeb2f3 100755
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -32,13 +32,13 @@
 
 notebooks_url = "https://github.com/huidongchen/simba_tutorials/raw/main/"
 notebooks = [
-    "rna_10xpmbc_all_genes",
-    "atac_buenrostro2018_peaks_and_sequences",
-    "multiome_shareseq",
-    "multiome_shareseq_GRN",
-    "rna_mouse_atlas",
-    "rna_human_pancreas",
-    "multiome_10xpmbc10k_integration",
+    "rna_10xpmbc_all_genes.ipynb",
+    "atac_buenrostro2018_peaks_and_sequences.ipynb",
+    "multiome_shareseq.ipynb",
+    "multiome_shareseq_GRN.ipynb",
+    "rna_mouse_atlas.ipynb",
+    "rna_human_pancreas.ipynb",
+    "multiome_10xpmbc10k_integration.ipynb",
 ]
 for nb in notebooks:
     try:
diff --git a/docs/source/index.rst b/docs/source/index.rst
index fbb134f..e7cc8dc 100755
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -1,4 +1,4 @@
-|Docs|
+|Docs| |Install with conda| |Lasst updated| |Downloads| |License|
 
 **SIMBA**: **SI**\ ngle-cell e\ **MB**\ edding **A**\ long with features
 ========================================================================
@@ -46,4 +46,18 @@ SIMBA is a method to embed cells along with their defining features such as gene
 
 
 .. |Docs| image:: https://readthedocs.org/projects/simba-bio/badge/?version=latest
-   :target: https://simba-bio.readthedocs.io
\ No newline at end of file
+   :target: https://simba-bio.readthedocs.io
+
+.. |Install with conda| image:: https://anaconda.org/bioconda/simba/badges/installer/conda.svg
+   :target: https://anaconda.org/bioconda/simba
+
+.. |Lasst updated| image:: https://anaconda.org/bioconda/simba/badges/latest_release_date.svg
+
+.. |License| image:: https://anaconda.org/bioconda/simba/badges/license.svg
+
+.. |Downloads| image:: https://anaconda.org/bioconda/simba/badges/downloads.svg
+
+
+
+
+