Merge branch 'main' into Ori-get_norm_func_property

scverse · Mar 6, 2025 · c04bc91 · c04bc91
2 parents 0279bd7 + bf8daf4
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diff --git a/docs/api/developer.md b/docs/api/developer.md
@@ -283,4 +283,5 @@ Utility functions used by scvi-tools.
    utils.setup_anndata_dsp
    utils.attrdict
    model.get_max_epochs_heuristic
+   external.decipher.utils.Trajectory
 ```
diff --git a/docs/references.bib b/docs/references.bib
@@ -222,12 +222,12 @@ @article{Martens2023
   publisher={Nature Publishing Group}
 }
 
-@article{Nazaret23,
-  title={Deep generative model deciphers derailed trajectories in acute myeloid leukemia},
-  author={Nazaret, Achille and Fan, Joy Linyue and Lavallee, Vincent-Philippe and Cornish, Andrew E and Kiseliovas, Vaidotas and Masilionis, Ignas and Chun, Jaeyoung and Bowman, Robert L and Eisman, Shira E and Wang, James and others},
+@article{Nazaret24,
+  title={Joint representation and visualization of derailed cell states with Decipher},
+  author={Nazaret, Achille and Fan, Joy Linyue and Lavall{\'e}e, Vincent-Philippe and Burdziak, Cassandra and Cornish, Andrew E and Kiseliovas, Vaidotas and Bowman, Robert L and Masilionis, Ignas and Chun, Jaeyoung and Eisman, Shira E and others},
   journal={bioRxiv},
   pages={2023--11},
-  year={2023},
+  year={2024},
   publisher={Cold Spring Harbor Laboratory},
   doi = {10.1101/2023.11.11.566719}
 }

diff --git a/docs/tutorials/index_scrna.md b/docs/tutorials/index_scrna.md
@@ -18,5 +18,6 @@ notebooks/scrna/contrastiveVI_tutorial
 notebooks/scrna/scanvi_fix
 notebooks/scrna/MrVI_tutorial
 notebooks/scrna/sysVI
+notebooks/scrna/decipher_tutorial
 notebooks/scrna/velovi
 ```
diff --git a/docs/user_guide/index.md b/docs/user_guide/index.md
@@ -48,6 +48,9 @@ scvi-tools is composed of models that can perform one or many analysis tasks. In
    * - :doc:`/user_guide/models/sysvi`
      - Integrating single-cell RNA-seq datasets with substantial batch effects
      - :cite:p:`Hrovatin23`
+   * - :doc:`/user_guide/models/decipher`
+     - Joint representation and visualization of derailed cell states with Decipher
+     - :cite:p:`Nazaret24`
    * - :doc:`/user_guide/models/velovi`
      - Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells
      - :cite:p:`GayosoWeiler23`

diff --git a/docs/user_guide/models/decipher.md b/docs/user_guide/models/decipher.md
@@ -0,0 +1,20 @@
+# Decipher
+
+:::{note}
+This page is under construction.
+:::
+
+**decipher** (Python class {class}`~scvi.external.Decipher`) is a ...
+
+The advantages of Decipher are:
+
+-   ...
+
+The limitations of Decipher include:
+
+-   ...
+
+```{topic} Tutorials:
+
+-   {doc}`/tutorials/notebooks/scrna/decipher_tutorial`
+```
diff --git a/src/scvi/external/decipher/_model.py b/src/scvi/external/decipher/_model.py
@@ -19,7 +19,7 @@
 
 
 class Decipher(PyroSviTrainMixin, BaseModelClass):
-    """Decipher model for single-cell data analysis :cite:p:`Nazaret23`.
+    """Decipher model for single-cell data analysis :cite:p:`Nazaret24`.
 
     Parameters
     ----------
@@ -238,7 +238,8 @@ def compute_decipher_time(
         cluster_obs_key : str
             The key in adata.obs containing cluster assignments.
         trajectory : Trajectory
-            A Trajectory object containing the trajectory information.
+            A :class:`~scvi.external.decipher.utils.Trajectory` object containing
+            the trajectory information.
         n_neighbors : int
             The number of neighbors to use for the KNN regression.
 
@@ -280,7 +281,8 @@ def compute_gene_patterns(
         adata : AnnData
             The annotated data matrix.
         trajectory : Trajectory
-            A Trajectory object containing the trajectory information.
+            A :class:`~scvi.external.decipher.utils.Trajectory` object containing
+            the trajectory information.
         l_scale : float
             The library size scaling factor.
         n_samples : int