Changelog

Changelog#

v1.0.0 2021-08-17#

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

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 immunce receptor chapters (#63) @drEast

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

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

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

  • Add compisitional analysis chapter (#89) @Zethson

  • Add lineage tracing chapter (#88) @mattjones315

  • Add preprocessing and visualizaton 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

  • Add new book CI (#57) @Zethson

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 environment CI (#158) @Zethson

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

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