CostaLab · ruthvik07 · Jul 3, 2025 · Jul 3, 2025 · Jul 3, 2025 · Jul 3, 2025
diff --git a/.DS_Store b/.DS_Store
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,3 @@
+test/test_check_with_R_data.py
+rawdata/snRNAseq_cellsWithSubtype.h5ad
+docs/source/notebooks/rawdata/snRNAseq_cellsWithSubtype.h5ad
diff --git a/README.md b/README.md
@@ -51,7 +51,8 @@ libgeos-dev
 ```
 
 
-## Features v1.0.1
+## Features v2.0.0
+
 
 - Single and Comparative Reports
    - Cell Cell Interaction visualization

diff --git a/dist/pycrosstalker-0.2.0-py3-none-any.whl b/dist/pycrosstalker-0.2.0-py3-none-any.whl
diff --git a/dist/pycrosstalker-0.2.0.tar.gz b/dist/pycrosstalker-0.2.0.tar.gz
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -6,3 +6,4 @@ plotly
 sphinx-rtd-size
 gprofiler-official
 sankeyflow
+nbformat
diff --git a/docs/source/Human_Myelofibrosis.md b/docs/source/Human_Myelofibrosis.md
@@ -0,0 +1,8 @@
+### pyCrossTalkeR Human Myelofibrosis Example
+
+```{toctree}
+---
+maxdepth: 3
+---
+notebooks/Human_Myelofibrosis.ipynb
+```
diff --git a/docs/source/Human_Myocardial_Infarction.md b/docs/source/Human_Myocardial_Infarction.md
@@ -0,0 +1,8 @@
+### pyCrossTalkeR Human Myocardial Infarction Example
+
+```{toctree}
+---
+maxdepth: 3
+---
+notebooks/Human_Myocardial_Infarction.ipynb
+```
diff --git a/docs/source/index.md b/docs/source/index.md
@@ -54,7 +54,8 @@ libgeos-dev
 ```
 
 
-## Features v1.0.1
+## Features v2.0.0
+
 
 - Single and Comparative Reports
    - Cell Cell Interaction visualization
@@ -80,7 +81,8 @@ libgeos-dev
 caption: Getting Started
 maxdepth: 2
 ---
-pyCrossTalkeR
+Human_Myelofibrosis
+Human_Myocardial_Infarction
 ```
 
 
@@ -91,4 +93,3 @@ caption: API Reference
 ---
 api
 ```
-
diff --git a/tutorials/pyCrossTalkeR.ipynb → ...ource/notebooks/Human_Myelofibrosis.ipynb b/tutorials/pyCrossTalkeR.ipynb → ...ource/notebooks/Human_Myelofibrosis.ipynb
diff --git a/docs/source/notebooks/Human_Myocardial_Infarction.ipynb b/docs/source/notebooks/Human_Myocardial_Infarction.ipynb
diff --git a/docs/source/notebooks/output/HMI_example/LR_data.pkl b/docs/source/notebooks/output/HMI_example/LR_data.pkl
diff --git a/docs/source/notebooks/output/HMI_example/LR_data_final.pkl b/docs/source/notebooks/output/HMI_example/LR_data_final.pkl
diff --git a/tutorials/output/LR_data.pkl → .../output/Myelofibrosis_example/LR_data.pkl b/tutorials/output/LR_data.pkl → .../output/Myelofibrosis_example/LR_data.pkl
diff --git a/tutorials/output/LR_data_final.pkl → ...t/Myelofibrosis_example/LR_data_final.pkl b/tutorials/output/LR_data_final.pkl → ...t/Myelofibrosis_example/LR_data_final.pkl
diff --git a/Test_Data/CTR_LR.csv → docs/source/notebooks/rawdata/CTR_LR.csv b/Test_Data/CTR_LR.csv → docs/source/notebooks/rawdata/CTR_LR.csv
diff --git a/Test_Data/CTR_LR_old.csv → docs/source/notebooks/rawdata/CTR_LR_old.csv b/Test_Data/CTR_LR_old.csv → docs/source/notebooks/rawdata/CTR_LR_old.csv
diff --git a/Test_Data/EXP_LR.csv → docs/source/notebooks/rawdata/EXP_LR.csv b/Test_Data/EXP_LR.csv → docs/source/notebooks/rawdata/EXP_LR.csv
diff --git a/Test_Data/EXP_LR_old.csv → docs/source/notebooks/rawdata/EXP_LR_old.csv b/Test_Data/EXP_LR_old.csv → docs/source/notebooks/rawdata/EXP_LR_old.csv
diff --git a/docs/source/notebooks/rawdata/ischemic_lr_liana_consensus.csv b/docs/source/notebooks/rawdata/ischemic_lr_liana_consensus.csv