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scATrans Documentation
Installation
Quickstart
Tutorials
Active Transcription Scoring on Real Spinal Cord Injury Data
scATrans without spliced/unspliced layers: differential expression + enrichment + plotting
User Guide
Core Workflow
Functional Enrichment
Visualization
Optional Advanced Features
Gene Feature Attachment & CLI
Standalone Differential Expression (no velocity data required)
Statistical Guidance & Reporting Checklist
API Reference
scatrans.active_score
scatrans.active_score_simple
scatrans.differential_expression
scatrans.differential_expression_simple
scatrans.diagnose_design
scatrans.recommend_workflow
scatrans.run_default_pipeline
scatrans.filter_active_genes
scatrans.store_raw_counts
scatrans.ensure_raw_counts
scatrans.restore_raw_counts
scatrans.add_gene_features
scatrans.generate_gene_features_from_gtf
scatrans.list_available_gene_features
scatrans.run_enrichment
scatrans.run_kegg
scatrans.run_go
scatrans.run_gsea
scatrans.simplify_enrichment
scatrans.save_enrichment_report
scatrans.expand_enrichment_genes
scatrans.list_bundled_gene_sets
scatrans.compare_enrichment
scatrans.extract_gene_lists
scatrans.concat_compare_results
scatrans.qc.unspliced_global
scatrans.pl.comet_plot
scatrans.pl.volcano_plot
scatrans.pl.volcano_3d
scatrans.pl.bias_diagnostic_plot
scatrans.pl.enrich_dotplot
scatrans.pl.enrich_barplot
scatrans.pl.enrich_upsetplot
scatrans.pl.enrich_vennplot
scatrans.pl.gseaplot
scatrans.pl.active_score_rankplot
scatrans.pl.active_genes_heatmap
scatrans.pl.velocity_phase_portraits
scatrans.pl.gamma_shrinkage_plot
scatrans.pl.set_style
scatrans.pl.set_nature_style
scatrans.pl.style_context
scatrans.pl.figure_export_context
scatrans.pl.save_all_figures
References & Data Sources
FAQ / Troubleshooting
Changelog
License
GitHub
Repository
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