# Changelog
## [v0.2.0](https://github.com/theislab/single-cell-best-practices/releases/tag/0.2.0) 2026-06-11
### Added
- Add env- and lamin-setup dropdown with `make dropdown`. ([#348](https://github.com/theislab/single-cell-best-practices/pull/348)) @LuisHenzlmeier
- Adding UMIs explanation figure ([#363](https://github.com/theislab/single-cell-best-practices/pull/363)) @LuisHeinzlmeier
- Add a style guide and chapter template for contributors ([#367](https://github.com/theislab/single-cell-best-practices/pull/367)) @LuisHeinzlmeier
- Update `scRNA-seq` chapter and add a paragraph on quantification of gene expression ([#371](https://github.com/theislab/single-cell-best-practices/pull/371)) @LuisHeinzlmeier
- Restructure the introduction into `fundamental` and `advanced` data structures and frameworks chapters ([#417](https://github.com/theislab/single-cell-best-practices/pull/417)) @LuisHeinzlmeier
- Add a figure style guide for contributors ([#420](https://github.com/theislab/single-cell-best-practices/pull/420)) @LuisHeinzlmeier
- Add a GPU acceleration chapter (`RAPIDS-singlecell`) ([#431](https://github.com/theislab/single-cell-best-practices/pull/431)) @Zethson
- Add intersphinx mapping and hyperlink API mentions throughout the book ([#441](https://github.com/theislab/single-cell-best-practices/pull/441)) @Zethson
- Mention GPU-accelerated alignment with NVIDIA Parabricks in the raw data processing chapter ([#446](https://github.com/theislab/single-cell-best-practices/pull/446)) @Zethson
### Changed
- Add dataset generator and update texts in `Interoperability` chapter. ([#347](https://github.com/theislab/single-cell-best-practices/pull/347)) @seohyonkim
- Update `make dropdown` by adding key takeaways dropdown and removing anchors ([#352](https://github.com/theislab/single-cell-best-practices/pull/352)) @LuisHeinzlmeier
- 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)) @seohyonkim
- Update dropdown chapter of `CONTRIBUTING.md` based on practical feedback ([#360](https://github.com/theislab/single-cell-best-practices/pull/360)) @LuisHeinzlmeier
- Use new connect syntax ([#404](https://github.com/theislab/single-cell-best-practices/pull/404)) @Zethson
- Update `10. Clustering` ([#406](https://github.com/theislab/single-cell-best-practices/pull/406)) @seohyonkim
- Use the proper dataset for `10. Clustering` ([#411](https://github.com/theislab/single-cell-best-practices/pull/411)) @seohyonkim
- Update `11. Annotation` ([#412](https://github.com/theislab/single-cell-best-practices/pull/412)) @seohyonkim
- Update `12. Data integration` ([#413](https://github.com/theislab/single-cell-best-practices/pull/413)) @seohyonkim
- Update `13. Pseudotemporal ordering` ([#414](https://github.com/theislab/single-cell-best-practices/pull/414)) @seohyonkim
- Update `14. RNA velocity` ([#415](https://github.com/theislab/single-cell-best-practices/pull/415)) @seohyonkim
- Update surface protein notebooks and key takeaways ([#423](https://github.com/theislab/single-cell-best-practices/pull/423)) @javier-marchena-hurtado
- Insert dropdowns for deployments ([#424](https://github.com/theislab/single-cell-best-practices/pull/424)) @Zethson
- Update the differential gene expression chapter ([#430](https://github.com/theislab/single-cell-best-practices/pull/430)) @LuisHeinzlmeier
- Add memory management details for `RAPIDS-singlecell` ([#432](https://github.com/theislab/single-cell-best-practices/pull/432)) @Zethson
### Fixed
- Pin `jupyter-book==1.0.4.post1` to restore compatibility after upstream v2 release broke PR preview and publish builds ([#400](https://github.com/theislab/single-cell-best-practices/pull/400)) @seohyonkim
- Fix precommit action to v3.0.0 ([#357](https://github.com/theislab/single-cell-best-practices/pull/357)) @seohyonkim
- Fix missed glossary links in `scRNA sequencing` and `raw data processing` ([#361](https://github.com/theislab/single-cell-best-practices/pull/361)) @seohyonkim
- Generating subset of human bmmcs and use it in chapter `10. Clustering` ([#410](https://github.com/theislab/single-cell-best-practices/pull/410)) @seohyonkim
- Minor factual fix ([#425](https://github.com/theislab/single-cell-best-practices/pull/425)) @ArchKudo
- Fix `scran` normalization to use raw counts for `computeSumFactors` ([#428](https://github.com/theislab/single-cell-best-practices/pull/428)) @matthiaspeterhans
- Update link for Cell Ranger output annotations ([#437](https://github.com/theislab/single-cell-best-practices/pull/437)) @Chloe-Shen
- Bound the `DataFrame` preview in the data-structures chapter ([#440](https://github.com/theislab/single-cell-best-practices/pull/440)) @Zethson
- Fix silently dropped citations by deduplicating BibTeX keys ([#442](https://github.com/theislab/single-cell-best-practices/pull/442)) @Zethson
- Fix invisible MuData/AnnData object summaries caused by a quiz CSS rule leaking `--pst-color-text-base: transparent` to all cell outputs ([#444](https://github.com/theislab/single-cell-best-practices/pull/444)) @Zethson
- Remove duplicated paragraph in section 6.5 ([#445](https://github.com/theislab/single-cell-best-practices/pull/445)) @durr1602
### Removed
- Remove the PR preview deployment from GitHub Actions ([#427](https://github.com/theislab/single-cell-best-practices/pull/427)) @Zethson
## [v0.1.0](https://github.com/theislab/single-cell-best-practices/releases/tag/0.1.0) 2023-11-14
### Added
- Add simpleaf example to the raw data processing section ([#116](https://github.com/theislab/single-cell-best-practices/pull/116)) @DongzeHE
- Add `inferring trajectories` section ([#101](https://github.com/theislab/single-cell-best-practices/pull/101)) @WeilerP
- Add `perturbation modelling` chapter ([#79](https://github.com/theislab/single-cell-best-practices/pull/79)) @Zethson
- Add Annotation ([#85](https://github.com/theislab/single-cell-best-practices/pull/85)) @LisaSikkema
- Add `gsea pathway` chapter ([#62](https://github.com/theislab/single-cell-best-practices/pull/62)) @soroorh
- Add `neighborhood analysis`, `spatial domains`, `spacially variable genes` chapters ([#86](https://github.com/theislab/single-cell-best-practices/pull/86)) @giovp
- Add `cell-cell communication` chapter ([#140](https://github.com/theislab/single-cell-best-practices/pull/140)) @dbdimitrov
- Add `paired integration` chapter ([#103](https://github.com/theislab/single-cell-best-practices/pull/103)) @alitinet
- Add multiple multimodal immunce receptor chapters ([#63](https://github.com/theislab/single-cell-best-practices/pull/63)) @drEast
- Add `spatial deconvolution` and `imputation` chapter ([#142](https://github.com/theislab/single-cell-best-practices/pull/142)) @AnnaChristina
- Add feedback from Robin Browaeys to `cell-cell comunication` chapter ([#157](https://github.com/theislab/single-cell-best-practices/pull/157)) @dbdimitrov
- Add docker container & improve environments ([#124](https://github.com/theislab/single-cell-best-practices/pull/124)) @Zethson
- Add `compisitional analysis` chapter ([#89](https://github.com/theislab/single-cell-best-practices/pull/89)) @Zethson
- Add `lineage tracing` chapter ([#88](https://github.com/theislab/single-cell-best-practices/pull/88)) @mattjones315
- Add `preprocessing and visualizaton` section ([#59](https://github.com/theislab/single-cell-best-practices/pull/59)) @AnnaChristina
- Add `clustering` chapter ([#72](https://github.com/theislab/single-cell-best-practices/pull/72)) @AnnaChristina
- Add PDF job ([#65](https://github.com/theislab/single-cell-best-practices/pull/65)) @Zethson
- Add `prior art` chapter ([#58](https://github.com/theislab/single-cell-best-practices/pull/58)) @Zethson
- Add new book CI ([#57](https://github.com/theislab/single-cell-best-practices/pull/57)) @Zethson
- Add `preamble` chapter ([#53](https://github.com/theislab/single-cell-best-practices/pull/53)) @Zethson
- Add scATAC part ([#162](https://github.com/theislab/single-cell-best-practices/pull/162)) @lauradmartens
- Add `modelling mechanism` section ([#96](https://github.com/theislab/single-cell-best-practices/pull/96)) @ilibarra
- Add `Integration` chapter ([#17](https://github.com/theislab/single-cell-best-practices/pull/17)) @lazappi
- Add new book CI ([#57](https://github.com/theislab/single-cell-best-practices/pull/57)) @Zethson
### Changed
- Fix typos ([#164](https://github.com/theislab/single-cell-best-practices/pull/164)) @mjstrumillo
- Correct 2 spelling mistakes ([#155](https://github.com/theislab/single-cell-best-practices/pull/155)) @namsaraeva
- Fix typos in chapter Normalization ([#118](https://github.com/theislab/single-cell-best-practices/pull/118)) @galicae
- Update `RNA velocity` chapter ([#100](https://github.com/theislab/single-cell-best-practices/pull/100)) @WeilerP
- Update `pseudotime` chapter ([#148](https://github.com/theislab/single-cell-best-practices/pull/148)) @WeilerP
- Update multimodal immune receptor chapters ([#110](https://github.com/theislab/single-cell-best-practices/pull/110)) @drEast
- Simplify `GSEA` chapter and improve performance ([#119](https://github.com/theislab/single-cell-best-practices/pull/119)) @ivirshup
- Improve `integration` chapter ([#109](https://github.com/theislab/single-cell-best-practices/pull/109)) @lazappi
- Update B-cell clonotype analysis ([#105](https://github.com/theislab/single-cell-best-practices/pull/105)) @jdhenaos
- Citeseq proofread ([#102](https://github.com/theislab/single-cell-best-practices/pull/102)) @cramsuig
- Review of analysis frameworks ([#98](https://github.com/theislab/single-cell-best-practices/pull/98)) @ivirshup
- Citeseq pp notebook ([#60](https://github.com/theislab/single-cell-best-practices/pull/60)) @danielStrobl
- Update `perturbation modeling` chapter ([#91](https://github.com/theislab/single-cell-best-practices/pull/91)) @yugeji
- Update `compositional analysis` chapter ([#76](https://github.com/theislab/single-cell-best-practices/pull/76)) @johannesostner
- Update `raw data processing` chapter ([#77](https://github.com/theislab/single-cell-best-practices/pull/77)) @DongzeHE
- Update `differential gene expression` chapter ([#80](https://github.com/theislab/single-cell-best-practices/pull/80)) @alitinet
- Update `preprocessing` section ([#139](https://github.com/theislab/single-cell-best-practices/pull/139)) @AnnaChristina
- Update `compositional analysis` chapter ([#149](https://github.com/theislab/single-cell-best-practices/pull/149)) @xinyuejohn
- Update `paired integration` and `advanced integration` chapter ([#135](https://github.com/theislab/single-cell-best-practices/pull/135)) @alitinet
- Improve pseudobulk plots for `differential gene expression` chapter ([#131](https://github.com/theislab/single-cell-best-practices/pull/131)) @alitinet
- Update `advanced integration` chapter ([#112](https://github.com/theislab/single-cell-best-practices/pull/112)) @alitinet
- Fix typos ([#166](https://github.com/theislab/single-cell-best-practices/pull/166)) @alitinet
- Update `compositional analysis` chapter according to changes of `pertpy` ([#152](https://github.com/theislab/single-cell-best-practices/pull/152)) @xinyuejohn
- Update link in `README.md` ([#107](https://github.com/theislab/single-cell-best-practices/pull/107)) @WeilerP
- Update `spatial deconvolution` chapter ([#93](https://github.com/theislab/single-cell-best-practices/pull/93)) @amitfrish
- Update `experimental data collection` chapter ([#71](https://github.com/theislab/single-cell-best-practices/pull/71)) @AnnaChristina
- Update `introduction` section ([#70](https://github.com/theislab/single-cell-best-practices/pull/70)) @AnnaChristina
- Update `preamble` ([#69](https://github.com/theislab/single-cell-best-practices/pull/69)) @AnnaChristina
### Fixed
- Fix broken link on edit button ([#115](https://github.com/theislab/single-cell-best-practices/pull/115)) @emiller88
- Fix environment CI ([#158](https://github.com/theislab/single-cell-best-practices/pull/158)) @Zethson
- Fix surface protein environment and small bugs ([#154](https://github.com/theislab/single-cell-best-practices/pulls/154)) @danielStrobl
- Add missing links to other chapters in `Compositional analysis` chapter ([#145](https://github.com/theislab/single-cell-best-practices/pull/145)) @dbdimitrov
- Fix environment CI ([#158](https://github.com/theislab/single-cell-best-practices/pull/158)) @Zethson
- Fix environments for `surface protein` section and small bugs ([#154](https://github.com/theislab/single-cell-best-practices/pull/154)) @danielStrobl