- deps: temporary fix copier breaks with pyyaml-include v2 (copier-org/copier1568) - docs: update FAQ.md with instructions for running pipeline on a cluster - deps: bump biopipen to 0.27.2 - fix(scrna.RadarPlots): fix mutaters not working - feat(tcr.CloneResidency): support `envs.upset_ymax` to set the max value of y axis in upset bar plot.
1.3.2
- deps: bump pipen to 0.14.5 - deps: add r-complexupset package to environment.yml and environment_full.yml for CloneResidency - deps: pin tensorflow to 2.15 for TESSA - deps: bump biopipen to 0.27.1 - depr(scrna.MarkersFinder): remove `envs.use_presto` as it's used by Seurat v5 by default - enh(tcr.CloneResidency): support log scale for y axis of upset bar plots - enh(scrna.SeuratClusterStats): allow to rotate labels in circos plot (pwwang/immunopipe48) <li.yingmayo.edu> - enh(scrna.SeuratClusterStats): use `pal_biopipen` for ident colors in circos plot - fix(scrna.CellsDistribution): fix the row order of the heatmaps - fix(scrna.SeuratClusterStats): fix when `envs.split-by` is specified - feat(scrna.CellsDistribution): support `envs.prefix_each` - feat(scrna.MarkersFinder): allow to set max number of genes to plot in dotplots - feat(scrna.MarkersFinder): support setting detailed arguments for overlapping plots - feat(scrna.MarkersFinder): support `envs.prefix_group` - feat(scrna.ScFGSEA): support `envs.prefix_each` - feat(scrna.RadarPlots): support `envs.prefix_each` and `envs.subset` - choir(scrna.SeuratClusterStats): use logger instead of print for log messages - choir(tcr.TCRClustering): print session info for `clustcr` script - choir(scrna.MarkersFinder): flatten toc when no `section` and no `ident-1` specified - docs: add more detailed docs for `envs.section` for multiple processes - BREAKING(scrna.SeuratMap2Ref): rename envs.name to envs.ident so envs.MapQuery.refdata is not - required anymore. It will be inferred from envs.ident and envs.use. <li.yingmayo.edu>
1.3.1
- deps: bump pipen to 0.14.3 - deps: pin ggplot2 to 3.4 for docker due to breaking changes of 3.5 - deps: bump biopipen to 0.26.2 - deps: bump datar-pandas to 0.5.5 to dismiss deprecated warnings - fix(utils.misc.R): replace latin and greek characters with closest ascii chars for slugify() - feat(scrna.TopExpressingGenes): support `subset` - fix(scrna.CellsDistribution): fix the row order of the heatmaps. - enh(tcr.CloneResidency): add legend for multiplets in upset plots. - feat(scrna.SeuratClusterStats): add circos plot for cell composition stats (46).
1.3.0
- deps: bump pipen to 0.14.1 - deps: bump pipen-report to 0.18.2 - deps: bump biopipen to 0.26.0 - fix(scrna.CellTypeAnnotation): keep factor meta data when input and output are RDS for celltypist - deps: bump datar to 0.15.4 (support pandas 2.2) - fix(utils.single_cell.R): fix `immdata_from_expanded` missing other data columns - fix(tcr.Immunarch): fix `mutaters` not working when no subset is set - fix(scrna.CellsDistribution): fix `hm_devpars` not working - fix(scrna.CellsDistribution): fix multiple `cells_by` columns and speed up plotting - choir(tcr.CloneResidency): mark singletons in Venn diagrams more clear - fix(scrna.RadarPlots): fix the order of groups on radar plots - choir(scrna.RadarPlots): transpose the count/percentage table to save to files - fix(scrna.MarkersFinder): fix generating report json file when no significant genes found - choir(scrna.MarkersFinder): Plot maximum 20 genes in dotplots - choir(scrna.MarkersFinder): Do not convert dashes in case names to dots - see more at <https://github.com/pwwang/biopipen/releases/tag/0.26.0>
1.2.0
- docs: update FAQs to align with Seurat v5 - docs: add image from manuscript to README.md - docs: center the flowchart image in README.md - docs: mention `celltypist` model prep in preparing input data - deps: bump pipen to 0.13.2 - deps: bump biopipen to 0.25.2: - scrna.MarkersFinder: allow to cache `FindAllMarkers` results - scrna.CellTypeAnnotation: support `celltypist` (pwwang/biopipen111) - scrna.SeuratSubClustering: add `envs_depth = 1` to replace whole `envs.cases` when new case assigned - scrna_metabolic_landscape.MetabolicPathwayHeterogeneit): fix output directory path is not slugified - tcr.Immunarch: change case filling log to debug level
1.1.1
- deps: Bump biopipen to 0.24.2 - chore: use internal slugify instead of slugify library - tcr.Immunarch: fix spectratyping output file extension is not png - scrna.SeuratPreparing: fix displaying filters in report - scrna.SeuratPreparing: fix logging Seurat procedure arguments