biopipen

What's Changed

• 0.2.0 by @pwwang in https://github.com/pwwang/biopipen/pull/23
  • 📌 Pin deps for docs
  • Don't link non-existing files for misc.Glob2Dir
  • Upgrade datar to 0.8
  • ⬆️ Upgrade pipen to v0.3
  • ⚡️ Load 10X TCR and RNA-seq data files more robustly for scrna.SeuratPreparing and tcr.ImmunarchLoading

Full Changelog: https://github.com/pwwang/biopipen/compare/0.1.9...0.2.0

• 🐛 Load all_config_annotations.csv if filtered_contig_annotations.csv doesn't exist for tcr.ImmunarchLoad
• 🐛 Calculate diversity for all clones only if filtering by clone sizes failed for tcr.ImmunarchAdvanced
• 🚑 Fix seurat object creating when expressions are named "Gene Expression" for scrna.SeuratPreparing
• ✨ Add tcr.TCRClustering
• ✨ Add raw to immdata for tcr.immunarchLoading
• ✨ Add on_raw env to tcr.TCRClustering
• ✨ Add bam.ControlFREEC

• ✨ Add tcr.Attach2Seurat

• ➕ Add datar dep for scrna_metabolic pipeline
• 🚑 Fix scrna_metabolic.MetabolicPathwayActivity
• ✨ Add bcftools.BcftoolsFilter
• 👽️ Don't wrap job report in report_jobs report macro (to adopt pipen-report 0.2)
• ✨ Add more options for scrna.DimPlots

• ✨ Convert CNVpytor results to gff and bed
• 🚑 Make scrna_metabolic pipeline work standalone
• ➕ Add datar dep for scrna_metabolic pipeline
• 🚑 Fix scrna_metabolic.MetabolicPathwayActivity
• ✨ Add bcftools.BcftoolsFilter

• ✨ Add features and fix issues for immunopipe 0.0.4
• ✨ Add some vcf processes

• 🐛 Fix bam.CNVpytor when snpfile is not provided
• ✨ Add metabolic pathway analysis for single-cell RNA-seq data

• Add gsea.GSEA and scrna.SCImpute
• Add gene name conversions
• Add gsea.FGSEA
• Add venn plots and refactor ImmunarchFilter
• Add plot.Heatmap
• Reuse plot.Heatmap for scrna.GeneExpressionInvestigation
• Attach metadata to seurat object in scrna.SeuratPreparing
• Add envs.group_subset for scrna.GeneExpressionInvestigation
• Fix typo for scrna.GeneExpressionInvestigation
• Add docs

• ✨ Add envs.qc for scrna.SeuratPreparing

• Finish processes for immunopipe

• Adopt pipen 0.2+