Modify readmle and docs

Author: drbecavin

README.md

@@ -45,17 +45,30 @@ https://checkatlas.readthedocs.io/en/latest/
 
 ## Examples
 
-1. Evaluate and compare different atlases: https://github.com/becavin-lab/checkatlas/blob/3a4f88e94716c09a3b9c86010f570743a5855461/examples/Atlas_comparison.ipynb
+### Example 1 - Evaluate and compare heterogenous scanpy atlases
 
-https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_1/CheckAtlas_example_1.html
+Evaluate and compare different atlases:
+[Example 1](CheckAtlas_example_1/Checkatlas_MultiQC.html)
 
-2. Evaluate different version of your atlas: https://github.com/becavin-lab/checkatlas/blob/3a4f88e94716c09a3b9c86010f570743a5855461/examples/Version_comparison.ipynb
+### Example 2 - Evaluate different version of the same atlas
 
-https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_2/CheckAtlas_example_2.html
+Evaluate different version of your atlas:
+[Example 2](CheckAtlas_example_2/Checkatlas_MultiQC.html)
 
-3. Explore Scanpy, Seurat and CellRanger objects in your folder: https://github.com/becavin-lab/checkatlas/blob/main/examples/AtlasType_comparison.ipynb
+### Example 3 - Evaluate Scanpy, Seurat and CellRanger atlases
+
+Evaluate Scanpy, Seurat and CellRanger objects in your folder:
+[Example 3](CheckAtlas_example_3/Checkatlas_MultiQC.html)
+
+### Example 4 - Evaluate post-process and raw atlases
+
+Evaluate an integrated Scanpy atlas with the corresponding raw CellRanger atlases:
+[Example 3](CheckAtlas_example_4/Checkatlas_MultiQC.html)
+
+### Example 5 - Avaluate different cellranger version atlases
+Evaluate different Cellranger atlases with multiple chemistry version and cellranger version:
+[Example 3](CheckAtlas_example_5/Checkatlas_MultiQC.html)
 
-https://checkatlas.readthedocs.io/en/stable/CheckAtlas_example_3/CheckAtlas_example_3.html
 
 ## Installation
 

docs/examples/examples.md

@@ -1,37 +1,37 @@
 # Examples
 
 A list of Checkatlas results on different atlases configuration
-## Example 1
+## Example 1 - Evaluate and compare heterogenous scanpy atlases
 
 Evaluate and compare different atlases:
 [Example 1](CheckAtlas_example_1/Checkatlas_MultiQC.html)
 
 This example has been generated with [1-Atlas_comparison.ipynb](jupyter/1-Atlas_comparison.ipynb) which you can downlad and run in checkatlas/examples/jupyter/ folder.
 
-## Example 2
+## Example 2 - Evaluate different version of the same atlas
 
 Evaluate different version of your atlas:
 [Example 2](CheckAtlas_example_2/Checkatlas_MultiQC.html)
 
 This example has been generated with [2-Version_comparison.ipynb](jupyter/2-Version_comparison.ipynb) which you can downlad and run in checkatlas/examples/jupyter/ folder.
 
-## Example 3
+## Example 3 - Evaluate Scanpy, Seurat and CellRanger atlases
 
-Explore Scanpy, Seurat and CellRanger objects in your folder:
+Evaluate Scanpy, Seurat and CellRanger objects in your folder:
 [Example 3](CheckAtlas_example_3/Checkatlas_MultiQC.html)
 
 This example has been generated with [3-AtlasType_comparison.ipynb](jupyter/3-AtlasType_comparison.ipynb) which you can downlad and run in checkatlas/examples/jupyter/ folder.
 
-## Example 4
+## Example 4 - Evaluate post-process and raw atlases
 
-Explore an integrate Scanpy atlas with the corresponding raw CellRanger atlas:
+Evaluate an integrated Scanpy atlas with the corresponding raw CellRanger atlases:
 [Example 3](CheckAtlas_example_4/Checkatlas_MultiQC.html)
 
 This example has been generated with [4-AtlasRawvsFinal_comparison.ipynb](jupyter/4-AtlasRawvsFinal_comparison.ipynb) which you can downlad and run in checkatlas/examples/jupyter/ folder.
 
-## Example 5
+## Example 5 - Avaluate different cellranger version atlases
 
-Explore different Cellranger atlases with multiple chemistry version and cellranger version:
+Evaluate different Cellranger atlases with multiple chemistry version and cellranger version:
 [Example 3](CheckAtlas_example_5/Checkatlas_MultiQC.html)
 
 This example has been generated with [5-CellRanger_comparison.ipynb](jupyter/5-CellRanger_comparison.ipynb) which you can downlad and run in checkatlas/examples/jupyter/ folder.

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "checkatlas"
-version = "0.3.10"
+version = "0.3.11"
 description="One liner tool to check the quality of your single-cell atlases."
 authors = ["becavin-lab"]
 readme = "README.md"