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

1.1.12

• fix(tcr.ScRepLoading): remove records with IG? or TR? chains to prevent errors in combineTCR and combineBCR
• chore(scrna.SeuratClusterStats): set default options for pies plot for stats
• fix(scrna.SeuratClusterStats): improve plot description handling when plot_type is not given

What's Changed

• 1.1.12 by @pwwang in #210

Full Changelog: 1.1.11...1.1.12

1.1.11

• refactor(stats.MetaPvalue1): optimize meta-analysis computation and improve performance
• feat(tcr.ScRepLoading): improve handling of contig file formats for 10X data
• feat(scrna.SeuratPreparing): add cell cycle scoring functionality to Seurat object preparation
• feat(scrna.SeuratPreparing): add cell cycle scoring arguments to SeuratPreparing
• feat(scrna.SeuratPreparing): set use_sct to FALSE by default for cell cycle scoring
• fix(scrna.MarkersFinder): improve plot argument handling for subset by group and plot types
• feat(tcr.ScRepLoading): support loading from prefixed contig files
• fix(scrna.CellTypeAnnotation): fix sctype not working

What's Changed

• 1.1.11 by @pwwang in #209

Full Changelog: 1.1.10...1.1.11

1.1.10

• fix(stats.MetaPvalue): adjust p-value adjustment calculation to use distinct records
• fix(stats.MetaPvalue1): adjust p-value adjustment calculation to use distinct id records
• feat(plot): add DensityPlot class for generating density plots
• feat: add version update functionality to Makefile
• fix(scrna.SeuratClusterStats): ensure either 'group_by' or 'ident' is specified in dimplots, not both

What's Changed

• 1.1.10 by @pwwang in #208

Full Changelog: 1.1.9...1.1.10

1.1.9

• fix(scrna.SeuratSubClustering): correct argument references in RunSeuratSubClustering function
• fix(scrna.SeuratClusterStats): handle reduction assignment for subclustering based on plot type and identity

What's Changed

• 1.1.9 by @pwwang in #207

Full Changelog: 1.1.8...1.1.9

1.1.8

• fix(scrna.SeuratClusterStats): fix dimplots for clusters from subclustering

What's Changed

• 1.1.8 by @pwwang in #206

Full Changelog: 1.1.7...1.1.8

1.1.7

• feat(scrna_metabolic_landscape): support multiple subset_by columns in Seurat object expansion
• chore: bump pipen-runinfo to 1.1.2

What's Changed

• 1.1.7 by @pwwang in #205

Full Changelog: 1.1.6...1.1.7

1.1.6

• fix(scrna.MarkersFinder): ensure proper handling of metadata and factor conversion in case processing to keep order of "each"
• fix(scrna.PseudoBulkDEG): ensure proper handling of metadata and factor conversion in case processing to keep order of "each"
• fix(scrna.ScFGSEA): ensure proper factor conversion for 'each' variable in case processing to keep order
• fix(scrna.TopExpressingGenes): ensure proper factor conversion for 'each' variable in case processing to keep order

What's Changed

• 1.1.6 by @pwwang in #204

Full Changelog: 1.1.5...1.1.6