pyro-ppl · fritzo · May 10, 2021 · Mar 24, 2021 · Mar 26, 2021 · Apr 11, 2021
diff --git a/2021-03-softplus_scales/cell2location_model.py b/2021-03-softplus_scales/cell2location_model.py
diff --git a/2021-03-softplus_scales/cell2location_model_numpyro.py b/2021-03-softplus_scales/cell2location_model_numpyro.py
diff --git a/2021-03-softplus_scales/cell2location_synthetic_data.ipynb b/2021-03-softplus_scales/cell2location_synthetic_data.ipynb
diff --git a/2021-03-softplus_scales/cell2location_synthetic_data_numpyro.ipynb b/2021-03-softplus_scales/cell2location_synthetic_data_numpyro.ipynb
diff --git a/2021-03-softplus_scales/environment_jax.yml b/2021-03-softplus_scales/environment_jax.yml
@@ -0,0 +1,38 @@
+name: numpyro
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - python = 3.7
+  - pip
+  - numpy >= 1.18.5
+  - pandas >= 1.0.4
+  - jupyter >= 1.0.0
+  - ipykernel >= 5.3.4
+  - leidenalg >= 0.8.0
+  - python-igraph >= 0.8.2
+  - nose >= 1.3.7
+  - scanpy >= 1.5.1
+  - scipy >= 1.4.1 
+  - louvain >= 0.6.1
+  - hyperopt >= 0.2.4
+  - loompy >= 2.0.16
+  - cmake >= 3.17.0
+  - dill >= 0.3.1
+  - ipython >= 7.15.0
+  - bbknn >= 1.3.9
+  - seaborn >= 0.10.1
+  - matplotlib >= 3.2.1
+  - request >= 2.83.1
+  - mkl-service >= 2.3.0
+  - pygpu >= 0.7.6
+  - cython >= 0.29.17
+  - pip:
+    - plotnine==0.7.0
+    - pymc3>=3.8,<3.10
+    - torch>=1.5.0
+    - pyro-ppl>=1.3.1
+    - git+https://github.com/BayraktarLab/cell2location.git
+    - git+https://github.com/pyro-ppl/numpyro.git
+    - jax
diff --git a/2021-03-softplus_scales/larger_data/cell2location_synthetic_data_5x_data.ipynb b/2021-03-softplus_scales/larger_data/cell2location_synthetic_data_5x_data.ipynb