biopipen

A set of processes/pipelines for bioinformatics

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biopipen - 0.27.4

Published by pwwang 6 months ago

  • feat: add plot.ROC
  • choir(delim.SampleInfo): add alpha to the colors of the plots using biopipen color pallete
  • feat: add snp.MatrixEQTL
  • docs(tcr/scrna/scrna_metabolic_landscape): update links of images in docs

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.27.3...0.27.4

biopipen - 0.27.3

Published by pwwang 7 months ago

  • deps: temporary fix copier breaks with pyyaml-include v2 (copier-org/copier#1568)
  • deps: bump pipen-poplog to 0.1.2 (quick fix for populating logs when job fails)
  • choir(scrna.ScFGSEA): Skip cases when no cells found (pwwang/immunopipe#50)
  • choir(scrna.MarkersFinder): Skip cases when no cells found (pwwang/immunopipe#50)
  • choir(scrna.MetaMarkers): Skip cases when no cells found (pwwang/immunopipe#50)
  • feat(scrna.SeuratPreparing): support DoubletFinder (pwwang/immunopipe#52)

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.27.2...0.27.3

biopipen - 0.27.2

Published by pwwang 7 months ago

  • fix(utils.misc.py): inherit envs when env passed for run_command()
  • 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.
  • feat(tcr.TCRDock): add process
  • choir(utils.misc.py): update level to DEBUG for python logger (leaving the filtering to pipen-poplog)
  • choir(stats.DiffCoexpr): change log_warn to debug for some verbosal logging messages
  • refactor(snp.PlinkSimulation): make the configuration files as input so multiple simulations could run in parallel easily.

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.27.1...0.27.2

biopipen - 0.27.1

Published by pwwang 7 months ago

  • 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.

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.27.0...0.27.1

biopipen - 0.27.0

Published by pwwang 7 months ago

  • deps: bump pipen to 0.14.5
  • deps: bump datar to 0.15.6
  • depr(scrna.MarkersFinder): remove 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/immunopipe#48)
  • 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 split-by is specified
  • feat(scrna.CellsDistribution): support prefix_each
  • feat(scrna.MarkersFinder): allow set max number of genes to plot in dotplots
  • feat(scrna.MarkersFinder): support setting detailed arguments for overlapping plots
  • feat(scrna.MarkersFinder): support prefix_group
  • feat(scrna.ScFGSEA): support prefix_each
  • feat(scrna.RadarPlots): support prefix_each and 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
  • choir: extract case expansion pattern (scrna.CellsDistribution, scrna.MarkersFinder, scrna.MetaMarkers, scrna.RadarPlots, scrna.ScFGSEA, scrna.TopExpressingGenes)
  • docs: add more detailed docs for envs.section
  • tests: add assertion for success of the pipelines
  • tests: add tests for utils.misc.R
  • tests: add r-presto to env_r.yml
  • tests: simplify tests for r functions
  • tests: pin scipy to 1.8.0 for clustcr in env_r.yml
  • tests: refactor tests for core.filters using unittest
  • tests: refactor tests for utils.common_docstrs using unittest
  • tests: refactor tests for utils.gene using unittest
  • tests: refactor tests for utils.mutate_helpers using unittest
  • tests: refactor tests for utils.single_cell using unittest

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.26.2...0.27.0

biopipen - 0.26.2

Published by pwwang 8 months ago

  • deps: bump datar-pandas to 0.5.5 to dismiss deprecated warnings

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.26.1...0.26.2

biopipen - 0.26.1

Published by pwwang 8 months ago

  • deps: bump pipen to 0.14.3
  • deps: pin ggplot2 to 3.4 due to breaking changes of 3.5 for test
  • 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 (pwwang/immunopipe#46).

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.26.0...0.26.1

biopipen - 0.26.0

Published by pwwang 8 months ago

  • deps: bump pipen to 0.14.1
  • deps: bump pipen-report to 0.18.1
  • 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 dashs in case names to dots
  • feat(utils.misc): add logger for python (which allows pipen-poplog to populate logs to running log)
  • feat: add rnaseq.UnitConversion and tests
  • feat: add rnaseq.Simulation to simulate RNAseq data
  • feat: add snp module and snp.PlinkSimulation process
  • feat: add stats module
  • feat: add stats.ChowTest
  • feat: add stats.LiquidAssoc
  • feat: add stats.DiffCoexpr
  • feat: add stats.MetaPvalue

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.25.4...0.26.0

biopipen - 0.25.4

Published by pwwang 9 months ago

  • 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

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.25.3...0.25.4

biopipen - 0.25.3

Published by pwwang 9 months ago

  • fix(scrna.CellTypeAnnotation): keep factor meta data when input and output are RDS for celltypist

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.25.2...0.25.3

biopipen - 0.25.2

Published by pwwang 9 months ago

  • fix(scrna_metabolic_landscape.MetabolicPathwayHeterogeneity): fix output directory path is not slugified
  • chore(tcr.Immunarch): change case filling log to debug level

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.25.1...0.25.2

biopipen - 0.25.1

Published by pwwang 9 months ago

  • scrna.CellTypeAnnotation: leave the meta data as is in celltypist wrapper

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.25.0...0.25.1

biopipen - 0.25.0

Published by pwwang 9 months ago

  • deps: bump pipen to 0.13.2
  • feat: add scrna.AnnData2Seurat and scrna.Seurat2AnnData
  • scrna.MarkersFinder: allow to cache FindAllMarkers results
  • scrna.CellTypeAnnotation: support celltypist (#111)
  • scrna.SeuratSubClustering: add envs_depth = 1 to replace whole envs.cases when new case assigned
  • test: add tests for celltypist of CellTypeAnnotation, AnnData2Seurat and Seurat2AnnData

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.24.2...0.25.0

biopipen - 0.24.2

Published by pwwang 9 months ago

  • deps: bump pipen-report to 0.17.3
  • chore: use internal slugify instead of slugify library
  • scrna.SeuratPreparing: fix displaying filters in report
  • scrna.SeuratPreparing: fix logging Seurat procedure arguments
  • cellranger: add CellRangerSummary
  • cell_ranger: use Iframe in report to have loading indicators
  • cellranger_pipeline: add CellRangerCountPipeline and CellRangerVdjPipeline

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.24.1...0.24.2

biopipen - 0.24.1

Published by pwwang 9 months ago

  • tcr.Immunarch: update spectratyping output file extension to png

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.24.0...0.24.1

biopipen - 0.24.0

Published by pwwang 9 months ago

  • deps: bump up deps by pipen 0.13
  • deps: add pipen-poplog to populate job logs to running log
  • deps: bump pipen-poplog to 0.0.2
  • feat: add utils.caching.R
  • cellranger: fix inferring sample name when fastqs from mulitple lanes
  • scrna.SeuratClustering/SeuratSubClustering: cache Seurat procedures step by step (pwwang/immunopipe#40)
  • scrna.MetaMarkers: limit log messages to be populated to 15
  • scrna.SeuratPreparing: log procedure arguments at debug level
  • scrna_metabolic_landscape.MetabolicFeaturesIntraSubset: use logger to log so can be poplutated to running log
  • scrna_metabolic_landscape.MetabolicPathwayActivity: use logger to log so can be poplutated to running log
  • tcr.ImmunarchLoading: add logs for steps
  • tcr.TCRClustering: use logger to log so can be poplutated to running log
  • tcr.TESSA: log command at debug level
  • tcr.Immunarch: add plot_type for divs to support boxplots
  • tcr.TCRClustering: fix log_info not found
  • tcr.Immunarch: make poplog_max 999 to pop all job logs to running log
  • scrna_metabolic_landscape.MetabolicFeaturesIntraSubset: change log level for groups from warning to info

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.8...0.24.0

biopipen - 0.23.8

Published by pwwang 10 months ago

  • scrna.SeuratPreparing: log Seurat procedure arguments
  • scrna.ScFGSEA: add subset to filter cells

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.7...0.23.8

biopipen - 0.23.7

Published by pwwang 10 months ago

  • scrna.SeuratPreparing: update log message for transformation/scaling step
  • scrna_metabolic_landscape.MetabolicPathwayHeterogeneity: add utils.gsea script source to support localizeGmtfile

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.6...0.23.7

biopipen - 0.23.6

Published by pwwang 10 months ago

  • feat: support url for gmtfile wherever GSEA is performed (#113)
  • utils.gsea.R: fix file path in gsea.R
  • tcr.Immunarch: add error message for empty filtered/subset data in diversity
  • scrna.SeuratPreparing: correct description of default assay in docstr
  • scrna.SeuratPreparing: run also the normal normalization procedures when SCTransform is used (useful for visualization purposes on RNA assay)
  • scrna.SeuratClustering: add related issue link to PrepSCTFindMarkers
  • scrna.ModuleScoreCalculator: document the names added by cell cycle score (pwwang/immunopipe#34)
  • scrna.SeuratPreparing: support sample names as reference for IntegrateLayers

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.5...0.23.6

biopipen - 0.23.5

Published by pwwang 10 months ago

  • scrna.SeuratClusterStats: fix when frac or frac_ofall is true and no group-by nor split-by is specified for stats
  • core.filters: fix when no enriched items found for report component enrichr
  • scrna.MarkersFinder: fix when no enriched items found
  • scrna.MetaMarkers: fix when no enriched items found
  • scrna.TopExpressingGenes: fix when no enriched items found
  • utils.gsea.R: fix when no enriched items found for runEnrichr
  • scrna_metabolic_landscript: fix adding report when ncores > 1

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.4...0.23.5

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