Update of Preprocessing and Visalization section (#356)

* update preprocessing yml

* update quality control

* finish quality control

* update normalization chapter

* update feature selection

* update dimensionality reduction

* update pre-commit to v3.0.0

* final touch

* Add changelog fragment

* fix dropdown to show in pdf

* change regex in quality control and rerun all the cells
Co-authored-by: KriBaLin <kribalin@users.noreply.github.com>
Co-authored-by: grst <mail@gregor-sturm.de>
Co-authored-by: adc0032 <clarkad@uab.edu>

* add citation to normalization chapter regarding issue #243

* fix doublet detection figure in quality contol regarding issue #244

* add explanation regarding issue #242 in quality control

* add one more citation in normalization

* A few minor changes

Signed-off-by: zethson <lukas.heumos@posteo.net>

* new image for doublet detection

* minor fixes

* more precise description in changelog fragment

---------

Signed-off-by: zethson <lukas.heumos@posteo.net>
Co-authored-by: zethson <lukas.heumos@posteo.net>

Author: seohyonkim

changelog.d/356.changed.md

@@ -0,0 +1 @@
+Load datasets via `lamindb`, use `localconverter` instead of `anndata2ri.activate()`, and add descriptions to the plots in `preprocessing and visualization` section ([#356](https://github.com/theislab/single-cell-best-practices/pull/356)) <sub>@seohyonkim</sub>

jupyter-book/_static/images/preprocessing_visualization/doublet_detection.jpeg

@@ -70,3 +70,28 @@ @article {Ahlmann-Eltze2023
 	eprint = {https://www.nature.com/articles/s41592-023-01814-1.pdf},
 	journal = {Nature Methods}
 }
+
+@article{lause2021,
+  title = {Analytic Pearson Residuals for Normalization of Single-Cell RNA-Seq UMI Data},
+  author = {Lause, Jan and Berens, Philipp and Kobak, Dmitry},
+  journal = {Genome Biology},
+  volume = {22},
+  number = {1},
+  pages = {258},
+  year = {2021},
+  month = sep,
+  issn = {1474-760X},
+  doi = {10.1186/s13059-021-02451-7},
+  url = {https://doi.org/10.1186/s13059-021-02451-7}
+}
+
+@article{norm:klebanoff2023_poisson_residuals,
+  title = {Normalization and gene selection for single-cell RNA-seq UMI data using sampling-adjusted sums of squares of Pearson residuals with a Poisson model},
+  author = {Klebanoff, Victor},
+  journal = {bioRxiv},
+  year = {2023},
+  month = dec,
+  doi = {10.1101/2023.12.21.572783},
+  url = {https://doi.org/10.1101/2023.12.21.572783},
+  note = {Preprint}
+}

jupyter-book/preprocessing_visualization/dimensionality_reduction.ipynb

@@ -3,19 +3,22 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - conda-forge::jupyterlab=3.5.0
-  - conda-forge::leidenalg=0.9.1
-  - conda-forge::numba=0.56.4
-  - conda-forge::python=3.9.15
-  - conda-forge::r-base=4.1.3
-  - conda-forge::r-soupx=1.6.1
-  - conda-forge::r-sctransform=0.3.3
+  - conda-forge::ipywidgets=8.1.5
+  - conda-forge::leidenalg=0.10.2
+  - conda-forge::numba=0.61.0
+  - conda-forge::python=3.12.9
+  - conda-forge::r-base=4.3.3
+  - conda-forge::r-soupx=1.6.2
+  - conda-forge::r-sctransform=0.4.1
   - conda-forge::r-glmpca=0.2.0
   - conda-forge::rpy2=3.5.11
-  - conda-forge::scanpy=1.9.3
+  - conda-forge::scanpy=1.11.1
   - conda-forge::session-info=1.0.0
-  - bioconda::anndata2ri=1.1
-  - bioconda::bioconductor-scdblfinder=1.8.0
-  - bioconda::bioconductor-scry=1.6.0
-  - bioconda::bioconductor-scran=1.22.1
-  - bioconda::bioconductor-glmgampoi=1.6.0
+  - bioconda::anndata2ri=1.3.2
+  - bioconda::bioconductor-scdblfinder=1.16.0
+  - bioconda::bioconductor-scry=1.14.0
+  - bioconda::bioconductor-scran=1.30.0
+  - bioconda::bioconductor-glmgampoi=1.14.0
+  - pip
+  - pip:
+      - lamindb[bionty,jupyter]