From 25ece7c66435b3d0907bdd76055f8ff3713a6bec Mon Sep 17 00:00:00 2001
From: Adam Gayoso <adamgayoso@users.noreply.github.com>
Date: Fri, 25 Mar 2022 08:10:39 -0700
Subject: [PATCH 1/2] Update references.rst

---
 docs/references.rst | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/docs/references.rst b/docs/references.rst
index 45380a139a..b037816d0d 100644
--- a/docs/references.rst
+++ b/docs/references.rst
@@ -1,6 +1,10 @@
 References
 ----------
 
+.. [Ashuach21] Tal Ashauch, Daniel A Reidenbach, Adam Gayoso, Nir Yosef (2022),
+   *PeakVI: A deep generative model for single-cell chromatin accessibility analysis*,
+   `Cell Reports Methods <https://doi.org/10.1016/j.crmeth.2022.100182>`__.
+
 .. [Gayoso22] Adam Gayoso*, Romain Lopez*, Galen Xing*, Pierre Boyeau, Valeh Valiollah Pour Amiri, Justin Hong, Katherine Wu, Michael Jayasuriya, Edouard Mehlman, Maxime Langevin, Yining Liu, Jules Samaran, Gabriel Misrachi, Achille Nazaret, Oscar Clivio, Chenling Xu, Tal Ashuach, Mohammad Lotfollahi, Valentine Svensson, Eduardo da Veiga Beltrame, Vitalii Kleshchevnikov, Carlos Talavera-Lopez, Lior Pachter, Fabian J Theis, Aaron Streets, Michael I Jordan, Jeffrey Regier, and Nir Yosef (2022),
    *A Python library for probabilistic analysis of single-cell omics data*,
    `Nature Biotechnology <http://dx.doi.org/10.1038/s41587-021-01206-w>`__.
@@ -13,10 +17,6 @@ References
    *Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation*,
    `biorxiv <https://www.biorxiv.org/content/10.1101/2021.04.28.441833v1>`__.
 
-.. [Ashuach21] Tal Ashauch, Daniel A Reidenbach, Adam Gayoso, Nir Yosef (2021),
-   *PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis*,
-   `biorxiv <https://www.biorxiv.org/content/10.1101/2021.04.29.442020v1>`__.
-
 .. [AshuachGabitto21] Tal Ashauch*, Mariano I Gabitto*, Michael I Jordan, Nir Yosef (2021),
    *MultiVI: deep generative model for the integration of multi-modal data*,
    `biorxiv <https://www.biorxiv.org/content/10.1101/2021.08.20.457057v1>`__.

From 8543fa621d421bbaa6893efca80d3b0d74707ea4 Mon Sep 17 00:00:00 2001
From: adamgayoso <adamgayoso@users.noreply.github.com>
Date: Fri, 25 Mar 2022 08:11:34 -0700
Subject: [PATCH 2/2] update handle

---
 docs/references.rst      | 2 +-
 docs/user_guide/index.md | 2 +-
 scvi/model/_peakvi.py    | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/references.rst b/docs/references.rst
index b037816d0d..01905c0df5 100644
--- a/docs/references.rst
+++ b/docs/references.rst
@@ -1,7 +1,7 @@
 References
 ----------
 
-.. [Ashuach21] Tal Ashauch, Daniel A Reidenbach, Adam Gayoso, Nir Yosef (2022),
+.. [Ashuach22] Tal Ashauch, Daniel A Reidenbach, Adam Gayoso, Nir Yosef (2022),
    *PeakVI: A deep generative model for single-cell chromatin accessibility analysis*,
    `Cell Reports Methods <https://doi.org/10.1016/j.crmeth.2022.100182>`__.
 
diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md
index 018322d2c5..80d71e9b62 100644
--- a/docs/user_guide/index.md
+++ b/docs/user_guide/index.md
@@ -50,7 +50,7 @@ scvi-tools is composed of models that can perform one or many analysis tasks. In
      - Reference
      - Tasks
    * - :doc:`/user_guide/models/peakvi`
-     - [Ashuach21]_
+     - [Ashuach22]_
      - Dimensionality reduction, removal of unwanted variation, integration across replicates, donors, and technologies, differential expression, imputation, normalization of other cell- and sample-level confounding factors
 ```
 
diff --git a/scvi/model/_peakvi.py b/scvi/model/_peakvi.py
index fbc25b5e9e..9c9ba59e23 100644
--- a/scvi/model/_peakvi.py
+++ b/scvi/model/_peakvi.py
@@ -35,7 +35,7 @@
 
 class PEAKVI(ArchesMixin, VAEMixin, UnsupervisedTrainingMixin, BaseModelClass):
     """
-    Peak Variational Inference [Ashuach21]_
+    Peak Variational Inference [Ashuach22]_
 
     Parameters
     ----------