Revision v1

.gitignore

@@ -5,3 +5,4 @@ notebooks/.ipynb_checkpoints
 .DS_Store
 .ipynb_checkpoints
 /notebooks/eval/cleaned/tests/data
+/tmp/

envs/csi_pip_req_minimal.txt

@@ -0,0 +1,32 @@
+# Do not forget to install csi package (current) after installing the following
+anndata==0.9.1
+colorcet==3.0.1
+joblib==1.1.1
+matplotlib==3.7.1
+networkx==2.8.4
+numpy==1.24.3
+pandas==1.5.3
+#rpy2==3.5.11
+sacred==0.8.4
+scanpy==1.9.3
+scipy==1.9.3
+seaborn==0.12.2
+seml==0.3.7
+setuptools==66.0.0
+statsmodels==0.13.5
+torch==1.13.1
+torchmetrics==0.11.4
+typing_extensions==4.5.0
+adjustText==0.8
+pytorch_lightning==1.6.5
+#scib-metrics==0.4.0
+#scib-metrics==0.5.1
+scib-metrics==0.3.3
+scvi-tools==0.17.3
+scikit-learn==1.2.2
+leidenalg==0.10.2
+jax==0.4.10
+jaxlib==0.4.10
+ml-dtypes==0.1.0
+harmonypy==0.0.10
+

envs/perturb_pip_req_minimal.txt

@@ -0,0 +1,28 @@
+scgen==2.1.0
+
+anndata==0.9.1
+colorcet==3.0.1
+joblib==1.1.1
+matplotlib==3.7.1
+networkx==2.8.4
+numpy==1.24.3
+pandas==1.5.3
+#rpy2==3.5.11
+sacred==0.8.4
+scanpy==1.9.3
+scipy==1.9.3
+seaborn==0.12.2
+seml==0.3.7
+setuptools==66.0.0
+statsmodels==0.13.5
+torch==1.13.1
+torchmetrics==0.11.4
+typing_extensions==4.5.0
+adjustText==0.8
+pytorch_lightning==1.6.5
+#scib-metrics==0.4.0
+scib-metrics==0.5.1
+scvi-tools==0.17.3
+scikit-learn==1.2.2
+
+

envs/pipelines_pip_req_minimal.txt

@@ -0,0 +1,5 @@
+pandas==1.5.3
+wandb==0.17.5
+seml=0.3.7
+numpy==1.24.3
+

envs/r_env_readme.txt

@@ -0,0 +1,21 @@
+# We used apptainer based on ml-verse
+```
+apptainer build --sandbox my_ml_verse docker://rocker/ml-verse
+```
+
+
+# Install python pacjages
+```
+pip install anndata
+```
+
+# Install R packages inside R:
+
+```
+install.packages("argparse")
+install.packages("Seurat")
+install.packages("harmony")
+install.packages("anndata")
+install.packages("reticulate")
+```
+

envs/scglue_pip_req_minimal.txt

@@ -0,0 +1,28 @@
+scglue==0.3.2
+
+anndata==0.9.1
+colorcet==3.0.1
+joblib==1.1.1
+matplotlib==3.7.1
+networkx==2.8.4
+numpy==1.24.3
+pandas==1.5.3
+#rpy2==3.5.11
+sacred==0.8.4
+scanpy==1.9.3
+scipy==1.9.3
+seaborn==0.12.2
+seml==0.3.7
+setuptools==66.0.0
+statsmodels==0.13.5
+torch==1.13.1
+torchmetrics==0.11.4
+typing_extensions==4.5.0
+adjustText==0.8
+pytorch_lightning==1.6.5
+#scib-metrics==0.4.0
+scib-metrics==0.5.1
+scvi-tools==0.17.3
+scikit-learn==1.2.2
+
+

envs/sysvi_pip_req_minimal.txt

@@ -0,0 +1,30 @@
+anndata==0.11.1
+colorcet==3.1.0
+joblib==1.4.2
+matplotlib==3.9.3
+networkx==3.4.2
+numpy==1.26.4
+pandas==2.2.3
+#rpy2
+sacred==0.8.7
+scanpy==1.10.4
+scipy==1.14.1
+seaborn==0.13.2
+seml==0.5.4
+statsmodels==0.14.4
+torch==2.5.1
+torchmetrics==1.6.0
+typing_extensions==4.12.2
+adjustText==1.3.0
+# pytorch_lightning
+#scib-metrics
+#scib-metrics
+scib-metrics==0.5.1
+# scvi-tools
+
+# git+https://github.com/Hrovatin/scvi-tools.git@main
+git+https://github.com/Hrovatin/scvi-tools.git@stable
+
+scikit-learn==1.6.0
+leidenalg==0.10.2
+