Changelog

v0.2.0 _2026-06-11¶

Added¶

• Add env- and lamin-setup dropdown with make dropdown. (#348) _{@LuisHenzlmeier}

• Adding UMIs explanation figure (#363) _{@LuisHeinzlmeier}

• Add a style guide and chapter template for contributors (#367) _{@LuisHeinzlmeier}

• Update scRNA-seq chapter and add a paragraph on quantification of gene expression (#371) _{@LuisHeinzlmeier}

• Restructure the introduction into fundamental and advanced data structures and frameworks chapters (#417) _{@LuisHeinzlmeier}

• Add a figure style guide for contributors (#420) _{@LuisHeinzlmeier}

• Add a GPU acceleration chapter (RAPIDS-singlecell) (#431) _@Zethson

• Add intersphinx mapping and hyperlink API mentions throughout the book (#441) _@Zethson

• Mention GPU-accelerated alignment with NVIDIA Parabricks in the raw data processing chapter (#446) _@Zethson

Changed¶

• Add dataset generator and update texts in Interoperability chapter. (#347) _@seohyonkim

• Update make dropdown by adding key takeaways dropdown and removing anchors (#352) _{@LuisHeinzlmeier}

• Load datasets via lamindb, use localconverter instead of anndata2ri.activate(), and add descriptions to the plots in Preprocessing and visualization section (#356) _@seohyonkim

• Update dropdown chapter of CONTRIBUTING.md based on practical feedback (#360) _{@LuisHeinzlmeier}

• Use new connect syntax (#404) _@Zethson

• Update 10. Clustering (#406) _@seohyonkim

• Use the proper dataset for 10. Clustering (#411) _@seohyonkim

• Update 11. Annotation (#412) _@seohyonkim

• Update 12. Data integration (#413) _@seohyonkim

• Update 13. Pseudotemporal ordering (#414) _@seohyonkim

• Update 14. RNA velocity (#415) _@seohyonkim

• Update surface protein notebooks and key takeaways (#423) _{@javier-marchena-hurtado}

• Insert dropdowns for deployments (#424) _@Zethson

• Update the differential gene expression chapter (#430) _{@LuisHeinzlmeier}

• Add memory management details for RAPIDS-singlecell (#432) _@Zethson

• Migrate to Jupyter Book v2 (#436) _@seohyonkim

Fixed¶

• Pin jupyter-book==1.0.4.post1 to restore compatibility after upstream v2 release broke PR preview and publish builds (#400) _@seohyonkim

• Fix precommit action to v3.0.0 (#357) _@seohyonkim

• Fix missed glossary links in scRNA sequencing and raw data processing (#361) _@seohyonkim

• Generating subset of human bmmcs and use it in chapter 10. Clustering (#410) _@seohyonkim

• Minor factual fix (#425) _@ArchKudo

• Fix scran normalization to use raw counts for computeSumFactors (#428) _{@matthiaspeterhans}

• Update link for Cell Ranger output annotations (#437) _@Chloe-Shen

• Bound the DataFrame preview in the data-structures chapter (#440) _@Zethson

• Fix silently dropped citations by deduplicating BibTeX keys (#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) _@Zethson

• Remove duplicated paragraph in section 6.5 (#445) _@durr1602

Removed¶

• Remove the PR preview deployment from GitHub Actions (#427) _@Zethson

v0.1.0 _2023-11-14¶

Added¶

• Add simpleaf example to the raw data processing section (#116) _@DongzeHE

• Add inferring trajectories section (#101) _@WeilerP

• Add perturbation modelling chapter (#79) _@Zethson

• Add Annotation (#85) _@LisaSikkema

• Add gsea pathway chapter (#62) _@soroorh

• Add neighborhood analysis, spatial domains, spacially variable genes chapters (#86) _@giovp

• Add cell-cell communication chapter (#140) _@dbdimitrov

• Add paired integration chapter (#103) _@alitinet

• Add multiple multimodal immune receptor chapters (#63) _@drEast

• Add spatial deconvolution and imputation chapter (#142) _{@AnnaChristina}

• Add feedback from Robin Browaeys to cell-cell communication chapter (#157) _@dbdimitrov

• Add docker container & improve environments (#124) _@Zethson

• Add compositional analysis chapter (#89) _@Zethson

• Add lineage tracing chapter (#88) _{@mattjones315}

• Add preprocessing and visualization section (#59) _{@AnnaChristina}

• Add clustering chapter (#72) _{@AnnaChristina}

• Add PDF job (#65) _@Zethson

• Add prior art chapter (#58) _@Zethson

• Add new book CI (#57) _@Zethson

• Add preamble chapter (#53) _@Zethson

• Add scATAC part (#162) _{@lauradmartens}

• Add modelling mechanism section (#96) _@ilibarra

• Add Integration chapter (#17) _@lazappi

Changed¶

• Fix typos (#164) (@mjstrumillo)

• Correct 2 spelling mistakes (#155) (@namsaraeva)

• Fix typos in chapter Normalization (#118) (@galicae)

• Update RNA velocity chapter (#100) (@WeilerP)

• Update pseudotime chapter (#148) (@WeilerP)

• Update multimodal immune receptor chapters (#110) (@drEast)

• Simplify GSEA chapter and improve performance (#119) (@ivirshup)

• Improve integration chapter (#109) (@lazappi)

• Update B-cell clonotype analysis (#105) (@jdhenaos)

• Citeseq proofread (#102) (@cramsuig)

• Review of analysis frameworks (#98) (@ivirshup)

• Citeseq pp notebook (#60) (@danielStrobl)

• Update perturbation modeling chapter (#91) (@yugeji)

• Update compositional analysis chapter (#76) (@johannesostner)

• Update raw data processing chapter (#77) (@DongzeHE)

• Update differential gene expression chapter (#80) (@alitinet)

• Update preprocessing section (#139) (@AnnaChristina)

• Update compositional analysis chapter (#149) (@xinyuejohn)

• Update paired integration and advanced integration chapter (#135) (@alitinet)

• Improve pseudobulk plots for differential gene expression chapter (#131) (@alitinet)

• Update advanced integration chapter (#112) (@alitinet)

• Fix typos (#166) (@alitinet)

• Update compositional analysis chapter according to changes of pertpy (#152) (@xinyuejohn)

• Update link in README.md (#107) (@WeilerP)

• Update spatial deconvolution chapter (#93) (@amitfrish)

• Update experimental data collection chapter (#71) (@AnnaChristina)

• Update introduction section (#70) (@AnnaChristina)

• Update preamble (#69) (@AnnaChristina)

Fixed¶

• Fix broken link on edit button (#115) (@emiller88)

• Fix environment CI (#158) (@Zethson)

• Fix surface protein environment and small bugs (#154) (@danielStrobl)

• Add missing links to other chapters in Compositional analysis chapter (#145) (@dbdimitrov)

• Fix environments for surface protein section and small bugs (#154) (@danielStrobl)