merge with master

.github/workflows/build_book.yml

@@ -8,10 +8,10 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Setup environment
         run: pip install --upgrade jupyter-book jupytext beautifulsoup4
@@ -37,10 +37,10 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Set up Python 3.9
-        uses: actions/setup-python@v3
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: "3.10"
 
       - name: Install Python dependencies
         run: |

.github/workflows/build_environments.yml

@@ -9,18 +9,25 @@ jobs:
       matrix:
         environments:
           [
-            "jupyter-book/introduction/analysis_tools_environment.yml",
-            "jupyter-book/preprocessing_visualization/preprocessing_environment.yml",
-            "jupyter-book/cellular_structure/clustering_environment.yml",
-            "jupyter-book/cellular_structure/integration_environment.yml",
-            "jupyter-book/conditions/compositional_environment.yml",
-            "jupyter-book/conditions/gsea_pathway_environment.yml",
-            "jupyter-book/conditions/perturbation_modeling_environment.yml",
-            "jupyter-book/trajectories/lineage_tracing_environment.yml",
-            "jupyter-book/trajectories/pseudotemporal_environment.yml",
+            "jupyter-book/introduction/analysis_tools.yml",
+            "jupyter-book/preprocessing_visualization/preprocessing.yml",
+            "jupyter-book/cellular_structure/clustering.yml",
+            "jupyter-book/cellular_structure/annotation.yml",
+            "jupyter-book/cellular_structure/integration.yml",
+            "jupyter-book/conditions/compositional.yml",
+            "jupyter-book/conditions/gsea_pathway.yml",
+            "jupyter-book/conditions/perturbation_modeling.yml",
+            "jupyter-book/conditions/differential_gene_expression.yml",
+            "jupyter-book/trajectories/lineage_tracing.yml",
+            "jupyter-book/trajectories/pseudotemporal.yml",
+            "jupyter-book/mechanisms/cell_cell_communication.yml",
+            "jupyter-book/spatial/spatial.yml",
+            "jupyter-book/surface_protein/surface_protein.yml",
+            "jupyter-book/multimodal_integration/paired_integration.yml",
+            "jupyter-book/multimodal_integration/advanced_integration.yml",
           ]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Install Conda environment with Micromamba
         uses: mamba-org/provision-with-micromamba@main

.github/workflows/publish_book.yml

@@ -17,7 +17,7 @@ jobs:
           python-version: 3.9
 
       - name: Setup environment
-        run: pip install --upgrade jupyter-book jupytext beautifulsoup4
+        run: pip install --upgrade jupyter-book==0.13.2 jupytext beautifulsoup4
 
       - name: Cache jupyter-cache folder
         uses: actions/cache@v2

.pre-commit-config.yaml

@@ -7,9 +7,15 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v2.6.2
+    rev: v2.5.1
     hooks:
       - id: prettier
+        # Newer versions of node don't work on systems that have an older version of GLIBC
+        # (in particular Ubuntu 18.04 and Centos 7)
+        # EOL of Centos 7 is in 2024-06, we can probably get rid of this then.
+        # See https://github.com/scverse/cookiecutter-scverse/issues/143 and
+        # https://github.com/jupyterlab/jupyterlab/issues/12675
+        language_version: "17.9.1"
   - repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:

README.md

@@ -1,11 +1,15 @@
 # Single-cell best practices
 
-![Cover](https://user-images.githubusercontent.com/21954664/204139606-c1f9f5bb-55ed-4fc9-9a12-e3ad1ebcb14f.png)
+![Cover](https://user-images.githubusercontent.com/21954664/217753288-080f727d-a5db-41d3-a439-ea5dbae1d1bc.png)
 
-> **Note**
-> This project and repository is under heavy development. However, many of the chapters are already in a good state, and we encourage interested readers to already start reading and to provide feedback.
->
-> A version of the book is rendered [here](https://sc-best-practices.org).
+The most recent version of the book is rendered [here](https://sc-best-practices.org).
+
+## Accompanying expert recommendation and citation
+
+This book builds upon our expert recommendation "Best practices for single-cell analysis across modalities": https://www.nature.com/articles/s41576-023-00586-w.
+If you found the expert recommendation or this book helpful for your research article please cite it as:
+
+> Heumos, L., Schaar, A.C., Lance, C. et al. Best practices for single-cell analysis across modalities. Nat Rev Genet (2023). https://doi.org/10.1038/s41576-023-00586-w
 
 ## Mission
 
@@ -14,13 +18,13 @@ We are writing a book on the current single-cell analysis best-practices with ex
 ## Contributing
 
 We would like to invite the community to further improve the tutorial and the teaching material.
-Please read [contributing](https://github.com/theislab/single-cell-best-practices/blob/development/CONTRIBUTING.md) for further instructions.
+Please read [contributing](https://github.com/theislab/single-cell-best-practices/blob/master/CONTRIBUTING.md) for further instructions.
 
 In case of questions or problems, please get in touch by posting an issue in this repository.
 
 ## Adapting the notebooks to other datasets:
 
-All notebooks for the various steps can be found in the [jupyter book folder](single-cell-best-practices/tree/master/jupyter-book) together with minimal Conda environments. Alternatively, the notebooks can be downloaded directly from the rendered version.
+All notebooks for the various steps can be found in the [jupyter book folder](https://github.com/theislab/single-cell-best-practices/blob/master/jupyter-book) together with minimal Conda environments. Alternatively, the notebooks can be downloaded directly from the rendered version.
 
 ## Acknowledgements
 

environment.yml

@@ -5,5 +5,5 @@ channels:
 dependencies:
   - conda-forge::python=3.10.6
   - conda-forge::jupyter-book==0.13.1
-  - conda-forge::jupytext==1.14.0
+  - conda-forge::jupytext==1.14.4
   - conda-forge::beautifulsoup4==4.11.1

jupyter-book/_config.yml

@@ -1,5 +1,5 @@
 title: Single-cell best practices
-author: Lukas Heumos, Anna Schaar
+author: Lukas Heumos, Anna Schaar, single-cell best practices consortium
 logo: logo.png
 
 description: >-
@@ -32,7 +32,7 @@ html:
   use_issues_button: true
   favicon: _static/favicon.ico
   comments:
-    hypothesis: true
+    hypothesis: false
   extra_footer: |
     <div>
       Brought to you by
@@ -70,22 +70,31 @@ bibtex_bibfiles:
   - preprocessing_visualization/normalization.bib
   - preprocessing_visualization/feature_selection.bib
   - preprocessing_visualization/dimensionality_reduction.bib
-  - cellular_structure/integration.bib
+  - cellular_structure/annotation.bib
   - cellular_structure/clustering.bib
+  - cellular_structure/integration.bib
   - trajectories/lineage_tracing.bib
   - trajectories/pseudotemporal.bib
+  - trajectories/rna_velocity.bib
   - conditions/differential_gene_expression.bib
   - conditions/compositional.bib
   - conditions/gsea_pathway.bib
   - conditions/perturbation_modeling.bib
+  - mechanisms/cell_cell_communication.bib
+  - mechanisms/gene_regulatory_networks.bib
   - deconvolution/bulk_deconvolution.bib
+  - chromatin_accessibility/introduction.bib
+  - chromatin_accessibility/quality_control.bib
+  - chromatin_accessibility/gene_regulatory_networks_atac.bib
   - surface_protein/references.bib
   - air_repertoire/references.bib
   - multimodal_integration/paired_integration.bib
   - multimodal_integration/advanced_integration.bib
+  - spatial/spatial.bib
 
 repository:
   url: https://github.com/theislab/single-cell-best-practices
+  path_to_book: jupyter-book
   branch: master
 
 binder:

jupyter-book/_toc.yml

@@ -9,7 +9,6 @@ parts:
       - file: introduction/scrna_seq
       - file: introduction/raw_data_processing
       - file: introduction/analysis_tools
-      - file: introduction/data_infrastructure
       - file: introduction/interoperability
   - caption: Preprocessing and visualization
     chapters:
@@ -20,6 +19,7 @@ parts:
   - caption: Identifying cellular structure
     chapters:
       - file: cellular_structure/clustering
+      - file: cellular_structure/annotation
       - file: cellular_structure/integration
   - caption: Inferring trajectories
     chapters:
@@ -34,14 +34,24 @@ parts:
       - file: conditions/perturbation_modeling
   - caption: Modeling mechanisms
     chapters:
-      - file: mechanisms/grns
+      - file: mechanisms/gene_regulatory_networks
       - file: mechanisms/cell_cell_communication
   - caption: Deconvolution
     chapters:
       - file: deconvolution/bulk_deconvolution
+  - caption: Chromatin Accessibility
+    chapters:
+      - file: chromatin_accessibility/introduction
+      - file: chromatin_accessibility/quality_control
+      - file: chromatin_accessibility/gene_regulatory_networks_atac
   - caption: Spatial omics
     chapters:
-      - file: spatial/motivation
+      - file: spatial/introduction
+      - file: spatial/neighborhood
+      - file: spatial/domains
+      - file: spatial/spatially_variable_genes
+      - file: spatial/deconvolution
+      - file: spatial/imputation
   - caption: Surface protein
     chapters:
       - file: surface_protein/quality_control
@@ -50,7 +60,7 @@ parts:
       - file: surface_protein/dimensionality_reduction
       - file: surface_protein/batch_correction
       - file: surface_protein/annotation
-  - caption: AIR repertoire
+  - caption: Adaptive immune receptor repertoire
     chapters:
       - file: air_repertoire/ir_profiling
       - file: air_repertoire/clonotype