1.2.7

• ci: update CACHE_NUMBER for conda environment to force updates
• feat(scrna.SeuratPreparing): add features parameter to LoadSeuratAndPerformQC for renaming features
• chore(deps): update r-base to version 4.4 in conda environment

What's Changed

• 1.2.7 by @pwwang in #220

Full Changelog: 1.2.6...1.2.7

1.2.6

• chore: bump xqute to 2.0.9 and pipen to 1.1.13
• docs(tcr.CDR3Clustering): add clarification on usage for TCR and BCR clustering
• fix(Makefile): update merge commit grep pattern in version rule

What's Changed

• 1.2.6 by @pwwang in #219

Full Changelog: 1.2.5...1.2.6

1.2.5

• chore(deps): bump pipen-board to 1.1.1 and pipen-report to 1.2.0
• chore(scrna.SeuratClusterStats): make 3d dimplots share assets
• chore(scrna.MarkersFinder): update plot dimensions for Dot Plot visualization

What's Changed

• 1.2.5 by @pwwang in #218

Full Changelog: 1.2.4...1.2.5

1.2.4

• chore(scrna): default envs.error flag to false for TopExpressingGenes, ScFGSEA, PseudoBulkDEG and MarkersFinder

What's Changed

• 1.2.4 by @pwwang in #217

Full Changelog: 1.2.3...1.2.4

1.2.3

• chore: bump pipen-report to 1.1.3 and pipen-poplog to 1.1.6
• test(scrna): add SubsetError case for Seurat process tests
• fix(scrna.PseudoBulkDEG): set default envs.error handling to True
• chore(scrna.MarkersFinder): defaut envs.error to True
• feat(scrna.PseudoBulkDEG): make envs.error control AggregateExpressionPseudobulk errors
• feat(scrna.ScFGSEA): add error handling for subsetting and filtering in ScFGSEA process
• feat(scrna.TopExpressingGenes): add error handling for subsetting cells
• feat(scrna.MarkersFinder): make envs.error control RunSeuratDEAnalysis errors
• docs(scrna.SeuratPreparing): add missing newline in docstring for clarity (immunopipe collapse followed options)
• docs(scrna.SeuratPreparing): enhance documentation for RNAData column paths and loading methods
• docs(scrna.SeuratMap2Ref): add detailed documentation for preparing Seurat reference for mapping

What's Changed

• 1.2.3 by @pwwang in #216

Full Changelog: 1.2.2...1.2.3

1.2.2

• feat(scrna.SeuratClusterStats): add 'add_box' parameter to ngenes_defaults for enhanced plotting options
• chore(scrna.MarkersFinder): add devpars for Dot Plot dimensions
• chore(scrna.SeuratClusterStats): remove commented default variable assignments for dimplots, features, and ngenes

What's Changed

• 1.2.2 by @pwwang in #215

Full Changelog: 1.2.1...1.2.2

1.2.1

• chore(cellranger): add output_flatten attribute to CellRangerCount and CellRangerVdj classes for flattened output directories
• chore(pipseeker.PipseekerFull): add output_flatten attribute to PipseekerFull class to make output directories flattened in process output directory
• chore: bump pipen to 1.1.12 (support output flattening for processes)
• chore(deps): bump diot to version 0.3.3 and python-simpleconf to version 0.9.2 (support templated configuration)

What's Changed

• 1.2.1 by @pwwang in #214

Full Changelog: 1.2.0...1.2.1

1.2.0

• chore: update commit log retrieval to use merge commit instead of last tag
• chore: bump pipen-report to 1.1.2
• style(tcr): clean up code style for python scripts
• chore: bump pipen to 1.1.10
• feat: add pipseeker pipeline with full and summary processes
• feat(scrna.ModuleScoreCalculator): add support for mouse cell cycle genes in module scoring
• docs(scrna.ModuleScoreCalculator): add additional arguments description for AddModuleScore and CellCycleScoring
• fix(regulatory): correct function calls to use biopipen.utils for height and width calculations in plot_variant_motifs
• feat: support relative devpars width/height for saving plots

What's Changed

• 1.2.0 by @pwwang in #213

Full Changelog: 1.1.14...1.2.0

1.1.14

• feat(scrna.SeuratClusterStats): support 3D dimplots
• chore: bump pipen-report to 1.1.1
• enh(scrna.SeuratClusterStats): improve dimensionality reduction plot description to include default identity context

What's Changed

• 1.1.14 by @pwwang in #212

Full Changelog: 1.1.13...1.1.14

1.1.13

• chore(deps): add umap-learn for Seurat's RunUMAP functionality in conda yml file
• feat(scrna.Seurat[Sub]Clustering): add python executable path for RunUMAP

What's Changed

• 1.1.13 by @pwwang in #211

Full Changelog: 1.1.12...1.1.13