Update Jupyter Book and names

README.md

@@ -1,6 +1,6 @@
 # RegVelo's reproducibility repository
 
-This repository contains the jupyter notebooks to reproduce results shown in [RegVelo: gene-regulatory-informed dynamics of single cells](https://doi.org/10.1101/2024.12.11.627935).
+This repository contains the jupyter notebooks to reproduce results shown in [RegVelo: gene-regulatory-informed dynamics of single cells](https://doi.org/10.1101/2024.12.11.627935) and has been rendered as a Jupyter book [here](https://theislab.github.io/regvelo_reproducibility/index.html).
 All datasets are freely available via a [FigShare project](https://figshare.com/account/home#/projects/226860).
 
 ## Installation

notebooks/_toc.yml

@@ -1,11 +1,30 @@
 format: jb-book
 root: index
 parts:
+    - caption: Cell cycle
+      chapters:
+          - file: cell_cycle/1_data_preparation.ipynb
+          - file: cell_cycle/2_regvelo.ipynb
+          - file: cell_cycle/2_scvelo.ipynb
+          - file: cell_cycle/2_velovi.ipynb
+          - file: cell_cycle/2_tfvelo.ipynb
+          - file: cell_cycle/2_unitvelo.ipynb
+          - file: cell_cycle/2_velovae_fullvb.ipynb
+          - file: cell_cycle/2_velovae.ipynb
+          - file: cell_cycle/2_cell2fate.ipynb
+          - file: cell_cycle/2_dpt.ipynb
+          - file: cell_cycle/2_celloracle.ipynb
+          - file: cell_cycle/2_grnboost2.ipynb
+          - file: cell_cycle/2_splicejac.ipynb
+          - file: cell_cycle/2_correlation.ipynb
+          - file: cell_cycle/3_comparison.ipynb
+          - file: cell_cycle/3_grn_influence.ipynb
+          - file: cell_cycle/3_grn_visualization.ipynb
     - caption: Pancreatic endocrinogenesis
       chapters:
           - file: pancreatic_endocrinogenesis/1_preprocessing.ipynb
           - file: pancreatic_endocrinogenesis/2_regvelo.ipynb
-          - file: pancreatic_endocrinogenesis/2_scveloipynb
+          - file: pancreatic_endocrinogenesis/2_scvelo.ipynb
           - file: pancreatic_endocrinogenesis/2_velovi.ipynb
           - file: pancreatic_endocrinogenesis/3_comparison_tsi.ipynb
           - file: pancreatic_endocrinogenesis/4_cell_fate_analysis.ipynb
@@ -14,15 +33,15 @@ parts:
           - file: pancreatic_endocrinogenesis/6_e2f1_targets_analysis.ipynb
           - file: pancreatic_endocrinogenesis/7_repeat_regvelo.ipynb
           - file: pancreatic_endocrinogenesis/8_perturbation_screening.ipynb
-          - file: pancreatic_endocrinogenesis/9_repeat_veloVI.ipynb
+          - file: pancreatic_endocrinogenesis/9_repeat_velovi.ipynb
           - file: pancreatic_endocrinogenesis/10_benchmark_identifiability.ipynb
           - file: pancreatic_endocrinogenesis/11_neurod2_analysis.ipynb
           - file: pancreatic_endocrinogenesis/11_screening_neurod2_targets.ipynb
     - caption: Hematopoiesis
       chapters:
           - file: hematopoiesis/1_preprocessing.ipynb
-          - file: hematopoiesis/2_regvelo_unregularized.ipynb
           - file: hematopoiesis/2_regvelo.ipynb
+          - file: hematopoiesis/2_regvelo_unregularized.ipynb
           - file: hematopoiesis/2_scvelo.ipynb
           - file: hematopoiesis/2_velovi.ipynb
           - file: hematopoiesis/3_comparison_gene_ranking.ipynb
@@ -42,10 +61,41 @@ parts:
           - file: zebrafish/2_velovi.ipynb
           - file: zebrafish/3_tsi_comparison.ipynb
           - file: zebrafish/4_driver_prediction.ipynb
+          - file: zebrafish/4_perturbation.ipynb
           - file: zebrafish/5_driver_prediction_comparison.ipynb
           - file: zebrafish/6_celloracle.ipynb
           - file: zebrafish/6_dynamo.ipynb
           - file: zebrafish/6_regvelo_perturbation.ipynb
           - file: zebrafish/7_perturbation_benchmark.ipynb
           - file: zebrafish/8_perturb_seq_analysis.ipynb
           - file: zebrafish/9_elf1_motif_analysis.ipynb
+    - caption: Toy GRN data
+      chapters:
+          - file: toy_grn/1_simulation.ipynb
+          - file: toy_grn/2_regvelo.ipynb
+          - file: toy_grn/2_scvelo.ipynb
+          - file: toy_grn/2_velovi.ipynb
+          - file: toy_grn/2_dpt.ipynb
+          - file: toy_grn/2_celloracle.ipynb
+          - file: toy_grn/2_grnboost2.ipynb
+          - file: toy_grn/2_correlation.ipynb
+          - file: toy_grn/3_comparison.ipynb
+          - file: toy_grn/3_plot_toy_simulation_benchmark.ipynb
+    - caption: Dyngen-simulated data
+      chapters:
+          - file: dyngen/1_data_conversion.ipynb
+          - file: dyngen/2_regvelo.ipynb
+          - file: dyngen/2_scvelo.ipynb
+          - file: dyngen/2_velovi.ipynb
+          - file: dyngen/2_unitvelo.ipynb
+          - file: dyngen/2_velovae_fullvb.ipynb
+          - file: dyngen/2_velovae.ipynb
+          - file: dyngen/2_cell2fate.ipynb
+          - file: dyngen/2_celloracle.ipynb
+          - file: dyngen/2_grnboost2.ipynb
+          - file: dyngen/2_splicejac.ipynb
+          - file: dyngen/2_correlation.ipynb
+          - file: dyngen/3_comparison.ipynb
+          - file: dyngen/3_velovi_benchmark.ipynb
+          - file: dyngen/3_regvelo_benchmark.ipynb
+          - file: dyngen/3_robustness_evaluation.ipynb

notebooks/dyngen/5_regvelo_benchmark.ipynb → notebooks/dyngen/3_regvelo_benchmark.ipynb

@@ -120,7 +120,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "DATASET = \"prior_benchmark\""
+    "DATASET = \"dyngen\""
    ]
   },
   {

notebooks/dyngen/6_robustness_evaluation.ipynb → notebooks/dyngen/3_robustness_evaluation.ipynb

@@ -113,7 +113,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "DATASET = \"prior_benchmark\""
+    "DATASET = \"dyngen\""
    ]
   },
   {

notebooks/dyngen/4_velovi_benchmark.ipynb → notebooks/dyngen/3_velovi_benchmark.ipynb

@@ -115,7 +115,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "DATASET = \"prior_benchmark\""
+    "DATASET = \"dyngen\""
    ]
   },
   {

notebooks/index.md

@@ -1,6 +1,6 @@
 # RegVelo's reproducibility repository
 
-This repository contains the jupyter notebooks to reproduce results shown in [RegVelo: gene-regulatory-informed dynamics of single cells](https://doi.org/10.1101/2024.12.11.627935).
+This repository contains the jupyter notebooks to reproduce results shown in [RegVelo: gene-regulatory-informed dynamics of single cells](https://doi.org/10.1101/2024.12.11.627935) and has been rendered as a Jupyter book [here](https://theislab.github.io/regvelo_reproducibility/index.html).
 All datasets are freely available via a [FigShare project](https://figshare.com/account/home#/projects/226860).
 
 ## Installation
@@ -16,7 +16,12 @@ pip install -e .
 python -m ipykernel install --user --name regvelo-py310 --display-name "regvelo-py310"
 ```
 
+## Data
+
+All datasets are freely available via a [FigShare project](https://figshare.com/account/home#/projects/226860). To run the provided analyses,
+download the corresponding data into the `data/` directory. For each dataset the directory `raw/` contains the data as obtained by the original study
+or in its raw format; similarly, in `processed/`, we collect all processed data.
+
 ## Remarks
 
--   Please install scvi-tools with version `0.20.3` ensure reproduce the results
 -   Results related to the in vivo Perturb-seq and multiome data analysis can be found [here](https://github.com/zhiyhu/neural-crest-scmultiomics)

scripts/dyngen/5_regvelo_benchmark.py → scripts/dyngen/3_regvelo_benchmark.py

@@ -37,7 +37,7 @@
 # ## Constants
 
 # %%
-DATASET = "prior_benchmark"
+DATASET = "dyngen"
 
 # %%
 SAVE_DATA = True

scripts/dyngen/6_robustness_evaluation.py → scripts/dyngen/3_robustness_evaluation.py

@@ -36,7 +36,7 @@
 # ## Constants
 
 # %%
-DATASET = "prior_benchmark"
+DATASET = "dyngen"
 
 # %%
 SAVE_FIG = True

scripts/dyngen/4_velovi_benchmark.py → scripts/dyngen/3_velovi_benchmark.py

@@ -32,7 +32,7 @@
 # ## Constants
 
 # %%
-DATASET = "prior_benchmark"
+DATASET = "dyngen"
 
 # %%
 SAVE_DATA = True