0.34.30

• chore(scrna.SeuratPreparing): adjust SCTransform parameters for improved data processing

What's Changed

• 0.34.30 by @pwwang in #193

Full Changelog: 0.34.29...0.34.30

0.34.29

• docs(scrna.CellTypeAnnotation): add support for celltypist in cell type annotations
• chore(deps): add mscorefonts to conda environment dependencies
• docs(scrna.SeuratClustering/SeuratSubClusering): add support for specifying features in UMAP arguments

What's Changed

• 0.34.29 by @pwwang in #192

Full Changelog: 0.34.28...0.34.29

0.34.28

• fix(misc): update require_package to use distribution for package checks
• feat(scrna.VireoSNP): add VireoSNP process for demultiplexing single-cell RNA-seq data
• fix(scrna.VireoSNP): update colormap retrieval method for consistency
• fix(scrna.VireoSNP): correct allele frequency matrix calculation to use dense array representation
• feat(scrna.VireoSNP): add plugin options for report generation
• fix(scrna.VireoSNP): correct job output directory reference in report generation
• fix(scrna.VireoSNP): improve clarity in clone identification description
• chore(deps): bump pipen, pydantic, varname, werkzeug, and xqute to latest versions
• chore(deps): update python version to 3.12 and add time dependency for pipen-runinfo
• chore(scrna.SeuratClusterStats): move dimplots to the front
• test(scrna.CellTypeAnnotation): add ModifyCellType process for cell type modification in Seurat
• fix(scrna.CellTypeAnnotation): improve handling of over_clustering assignment from Seurat object for celltypist
• chore(deps): specify version for clustcr to avoid old versions
• chore(deps): update conda channels for biopipen environment
• chore(deps): downgrade python version to 3.11 in biopipen environment

What's Changed

• 0.34.28 by @pwwang in #191

Full Changelog: 0.34.27...0.34.28

0.34.27

• chore(deps): bump pipen-report to 0.23.15
• feat(tcr.CDR3Clustering): add verbose output option for GIANA command
• fix(scrna.AnnData2Seurat): resolve issue with pdf device not opening correctly for dotplot generation
• fix(scrna.CellTypeAnnotation): update package requirement from celltypist to celltypist2 (a version adopts numpy v2)
• fix(tcr.GIANA): update length dictionary to allow a wider range of sequence lengths
• fix(tcr.TESSA): add Keras model migration support for v2 and v3
• test(tcr.CDR3Clustering): add CDR3Clustering tests for ClusTCR and GIANA tools

What's Changed

• 0.34.27 by @pwwang in #190

Full Changelog: 0.34.26...0.34.27

0.34.26

• chore(docker): clean up conda package cache after installations
• chore(docker): update CellRanger base image to version 10.0.0
• feat(scrna): add CellSNPLite and MQuad processes for single-cell SNP analysis
• docs(cellranger_pipeline): update documentation for CellRanger pipeline to reflect new version
• ci: add step to delete cache for space optimization
• chore(deps): comment out r-immunarch dependency in environment file
• enh(misc): enable line buffering for stdout/stderr when redirecting to files or pipes
• chore(deps): add pipen-log2file as an optional dependency

What's Changed

• 0.34.26 by @pwwang in #189

Full Changelog: 0.34.25...0.34.26

0.34.25

• fix(scrna.PseudoBulkDEG): change default assay from "RNA" to None so that default assay can be used by default
• feat(scrna.ScFGSEA): add assay parameter to allow specification of assay in analysis
• fix(scrna.CellTypeAnnotation): correct assignment of identities in rename_idents function

What's Changed

• 0.34.25 by @pwwang in #188

Full Changelog: 0.34.24...0.34.25

0.34.24

• feat(tcr.ClonalStats): add save_data parameter to ClonalStats for saving plot data
• docs(scrna): add link to additional databases in multiple classes for enrichment analysis

What's Changed

• 0.34.24 by @pwwang in #187

Full Changelog: 0.34.23...0.34.24

0.34.23

• docs(scrna.CellTypeAnnotation): clarify renaming of original identity column during cell type annotation
• chore: bump up dependencies in poetry.lock

What's Changed

• 0.34.23 by @pwwang in #186

Full Changelog: 0.34.22...0.34.23

0.34.22

• chore(scrna): update future.globals.maxSize to Inf for improved memory handling
• feat(tcr.CDR3Clustering): rename TCRClustering to CDR3Clustering and adopt BCR data
• ci(docker): add cache deletion step to save space in Docker workflows

What's Changed

• 0.34.22 by @pwwang in #185

Full Changelog: 0.34.21...0.34.22

0.34.21

• fix(cellranger.CellRangerCount): ensure reference path exists before processing
• chore(docker/cellranger_pipeline): ensure telemetry is disabled for cellranger in Dockerfile
• chore(cellranger.CellRangerCount): print detected cellranger version for better debugging
• docs(cellranger_pipeline): update reference URLs for clarity and consistency
• feat(cellranger.CellRangerVdj): add support for handling mounted output directories
• ci(docker): update Dockerfiles to use 'latest' tag for base images
• ci: simplify conditions for docker-test, docker-cnvkit-pipeline, and docker-cellranger-pipeline jobs
• ci: update conditions in docker workflow to use join for modified files
• fix(cellranger.CellRangerVdj): exclude additional environment variables in CLI arguments
• ci(docker): change condition for checking changes to use logical AND
• fix(cellranger.CellRangerVdj): handle exceptions during output copying to ensure essential files exist
• feat(cellranger.CellRangerCount): handle output directory issues for mounted filesystems
• feat(cellranger.CellRangerVdj): print version of cellranger in stdout
• docs(scrna): update dbs/gmtfile parameter description for enrichment analysis
• chore: bump biopipen-board to 0.17.3

What's Changed

• 0.34.21 by @pwwang in #184

Full Changelog: 0.34.20...0.34.21