Change Log

1.4.3

  • deps: update pipen-runinfo dependency to version 0.8.0 (pipen to 0.15.2)
  • deps: update biopipen dependency to version 0.31.4
  • fix(scrna.SeuratMap2Ref): fix refnorm not detected for NormlizeData'ed reference

1.4.2

  • deps: add bioconductor-destiny dependency in docker environment files for ModuleScoreCalculator

1.4.1

  • docs: update tutorial dataset information and links

1.4.0

  • docs: update Singularity and Apptainer commands to include --writable-tmpfs flag
  • docs: allow collapsing ns/choice items in the docs for processes
  • docker: update Dockerfile to include npm cache configuration to allow the pipeline to run on read-only file system
  • tests: update SeuratPreparing config to use DoubletFinder for doublet detection
  • ci: use latest actions
  • deps: add r-clustree as a dependency in docker environment files
  • deps: update dependencies in docker environment files (python3.10, R4.3)
  • deps: bump biopipen to 0.29.0
  • fix(tcr.TCRClusterStats): fix envs.shared_clusters.heatmap_meta being broken by envs.shared_clusters.sample_order (@li.ying@mayo.edu)
  • choir(scrna.SeuratMap2Ref): present better error message when envs.use or values of envs.MapQuery.refdata not in reference (@li.ying@mayo.edu)
  • fix(scrna.MarkersFinder): run PrepSCTFindMarkers when needed
  • choir(scrna.SeuratClustering): use FindClusters to run for multiple resolutions
  • choir(scrna.SeuratSubClustering): use FindClusters to run for multiple resolutions
  • feat(scrna.SeuratClustering): add clustree plot (@li.ying@mayo.edu)
  • feat(scrna.SeuratSubClustering): add clustree plot
  • tests(scrna.SeuratClusterStats): add assertion for clustree plot generation
  • deps: bump biopipen to 0.29.1
  • fix(delim.SampleInfo): fix numbers not split up when each is specified.
  • enh(delim.SampleInfo): make sizes of pie charts proportional to number of samples when each is specified
  • enh(scrna.MarkersFinder): run PrepSCTFindMarkers when necessary before calling FindMarkers
  • feat(scrna.SeuratPreparing): add option to cache Seurat object at different steps
  • feat(scrna.SeuratPreparing): allow doubletfinder to run with a different number of cores
  • chore(scrna.SeuratClustering): record PrepSCTFindMarkers command in sobj@commands
  • tests(scrna.SeuratClusterStats): use less stringent p-value cutoff for DEG/MarkersFinder
  • tests(scrna.SeuratPreparing): add doubletfinder in tests
  • deps: bump biopipen to 0.29.2
  • chore(scrna.SeuratClusterStats): use ident label length to adjust default height for feature plots
  • fix(scrna.MetaMarkers): fix seurat object not updated when expanding cases and run PrepSCTFindMarkers when necessary before calling meta-markers
  • fix(scrna.MarkersFinder): fix fetching command when composing the PrepSCTFindMarkers command
  • fix(scrna_metabolic_landscape): handle null values in for loop in MetabolicFeatures and MetabolicFeaturesIntraSubset for report generation
  • deps: bump biopipen to 0.30.0
  • BREAKING(scrna): move clustree plots from SeuratClustering/SeuratSubClustering to SeuratClusterStats
  • feat(scrna.CellTypeAnnotation): allow to merge/not to merge (envs.merge) the clusters with the same labels predicted
  • feat(scrna.SeuratPreparing): add scDblFinder to detect doublets
  • feat(scrna.SeuratMap2Ref): add envs.skip_if_normalized option to skip normalization if query is already normalized using the same - method as the reference
  • refactor(tcr.Immunarch): source the files for Immunarch scripts for better debugging
  • refactor(scnra.SeuratClustering): refactor the script for better debugging
  • refactor(scnra.SeuratPreparing): refactor the script for better debugging
  • fix(scrna): fix resolution expansion for SeuratClustering and SeuratSubClustering
  • fix(scrna): Fix generating PrepSCTFindMarkers command when no previous commands present
  • tests(scrna.ScFGSEA): fix unavailable urls to GMT files
  • chore(scrna.SeuratMap2Ref): optimize memory usage
  • chore(scrna.MetaMarkers): remove plugin_opts.poplog_max
  • chore(tcr.CloneResidency): improve logging when handling subjects
  • deps: bump biopipen to 0.31.3
  • enh(scrna.SeuratMap2Ref): check if reference has SCTModel if SCTransform'ed (likely prepared by old Seurat)
  • fix(tcr.CDR3AAPhyschem): use sequence from TRB chain only
  • fix(tcr.CDR3AAPhyschem): fix when chain is not available
  • fix(tcr.TCRClustering): fix for multi-chain TCRs, use TRB only if on_multi is false
  • fix(tcr.TCRClustering): fix when chain is not available

1.3.9

  • docs: update docs for TCellSelection to avoid confusion
  • deps: bump biopipen to 0.27.9
  • feat(tcr.TCRClusterStats): add sample_order to set sample order on heatmap and cluster_rows to switch row clustering on/off

1.3.8

  • docs: remove -w option for apptainer/singularity as no writing is necessary since pipen-board 0.15.1
  • deps: update biopipen to version 0.27.8
  • fix(scrna.SeuratClusterStats): fix selected columns not unique for stats
  • feat(scrna.SeuratMap2Ref): allow non-SCTransform'ed reference
  • feat(scrna.SeuratMap2Ref): allow splitting query object for mapping (pwwang/immunopipe#61)
  • deps: update pipen-board to version 0.15.1 (allow configuration file path in the URL box on Web UI)

1.3.7

  • ci: fix docker images building when no essential changes made

1.3.6

  • ci: fix deploy workflow (#59)
  • ci: add README.md to tests-output branch
  • ci: fix test/test workflow
  • tests: add make test
  • tests: init test data preparation
  • tests: add test for ImmunarchLoading
  • tests: add tests for SeuratPreparing
  • tests: Update configs for SeuratPreparing test to subset cells so tests can run on CI
  • tests: update SeuratPreparing test to disable export
  • tests: add tests for SeuratClusteringOfAllCells/SeuratClustering
  • docs: update installation instructions (@stein.mariam@mayo.edu)
  • deps: bump biopipen to version 0.27.7 (0.27.5-0.27.7)
  • fix(scrna.SeuratClusterStats): fix color palette for ridge plots (@stein.mariam@mayo.edu)
  • feat(scrna.SeuratPreparing): add envs.cell_qc_per_sample to filter cells before merging instead after
  • fix(scrna_metabolic_landscape.MetabolicFeatures): fix return value of groups with less than 5 cells in do_one_group
  • fix(scrna_metabolic_landscape): fix mutaters not working.
  • fix(scrna_metabolic_landscape.MetabolicFeatures/MetabolicFeaturesIntraSubset): skip groups with less than 5 cells in do_one_group and save a warning file under the case
  • chore: fix typo in class name ExprImpution to ExprImputation

1.3.5

  • ci/test: add tests in CI and deploy output in a different branch
  • deps: bump biopipen to 0.27.4
  • choir(delim.SampleInfo): add alpha to the colors of the plots using biopipen color pallete
  • docs(tcr/scrna/scrna_metabolic_landscape): update links of images in docs

1.3.4-post

  • ci/test: init ci for tests
  • docs: introduce versioning for docs

1.3.4

  • deps: bump biopipen to 0.27.3
  • deps: bump pipen-poplog to 0.1.2 (quick fix for populating logs when job fails)
  • deps: temporary fix copier breaks with pyyaml-include v2 (copier-org/copier#1568)
  • choir(scrna.ScFGSEA): Skip cases when no cells found (#50)
  • choir(scrna.MarkersFinder): Skip cases when no cells found (#50)
  • choir(scrna.MetaMarkers): Skip cases when no cells found (#50)
  • feat(scrna.SeuratPreparing): support DoubletFinder (#52)

1.3.3

  • deps: temporary fix copier breaks with pyyaml-include v2 (copier-org/copier#1568)
  • 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/immunopipe#48) @li.ying@mayo.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.ying@mayo.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/biopipen#111)
  • 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

1.1.0

  • docs: update table in gallery
  • deps: use pipen-poplog to populate job logs to pipeline running log
  • deps: bump biopipen to 0.24. Hights:
  • scrna.ScFGSEA: add subset to filter cells (pwwang/biopipen#112) @yuey11
  • scrna.SeuratClustering/SeuratSubClustering: cache Seurat procedures step by step (#40) @xyfqwlzoe
  • tcr.Immunarch: add plot_type to support boxplots for diversity metrics
  • see more at https://github.com/pwwang/biopipen/releases/tag/0.24.0

1.0.5

  • change: do not rescale gene expression in TCellSelection any more
  • fix: fix column names of indicators not aligned with indicator_genes
  • feat: add feature plots in TCellSelection
  • deps: bump biopipen to 0.23.8
  • scrna.SeuratPreparing: log Seurat procedure arguments
  • scrna.ScFGSEA: add subset to filter cells (pwwang/biopipen#112)

1.0.4

  • deps: bump biopipen to 0.23.7
  • scrna.SeuratPreparing: update log message for transformation/scaling step
  • scrna_metabolic_landscape.MetabolicPathwayHeterogeneity: add utils.gsea script source to support localizeGmtfile

1.0.3

  • deps: add r-seuratdisk dependency to conda env files. @yuey11
  • deps: pin r-matrixstats to 1.1.0 in conda env files to fix useNames = NA error. @yuey11
  • refactor: optimize configuration file validation
  • deps: bump biopipen to 0.23.6
  • feat: support url for gmtfile wherever GSEA is performed (pwwang/biopipen#113)
  • 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.ModuleScoreCalculator: document the names added by cell cycle score (#34)
  • scrna.SeuratPreparing: support sample names as reference for IntegrateLayers

1.0.2

  • deps: add bioconductor-glmgampoi to conda env files (#33)
  • docs: correct the Seurat object assay description
  • deps: bump biopipen to 0.23.5
  • fix: fix when no enriched items found for scrna.MarkersFinder, scrna.MetaMarkers and scrna.TopExpressingGenes
  • scrna.SeuratClusterStats: fix when frac or frac_ofall is true and no group-by nor split-by is specified for stats
  • utils.gsea.R: fix when no enriched items found for runEnrichr
  • scrna_metabolic_landscript: fix adding report when ncores > 1

1.0.1

  • docs: add gallery section to README.md
  • change: set default nstart of kmeans to 25 in TCellSelection
  • deps: add r-hdf5r in conda env files to support Read_10x_h5 from Seurat. @yuey11
  • deps: bump biopipen to 0.23.4
  • scrna.TopExpressingGenes: fix colnames while pulling average expression
  • scrna.CellsDistribution: fix when cells_by has multiple column names
  • scrna.CellTypeAnnotation: fix the order of the clusters for direct method
  • scrna.SeuratClusterStats: add position options for bar plots for stats
  • scrna.RadarPlots: add colors to set the colors of the loops in radar and bar plots
  • tcr.Immunarch: add split_by and split_order to put subplots together in one single plots

1.0.0

Highlights

  • feat: support Seurat v5 (integration is now down by Seurat::IntegrateLayers)
  • feat: support supervised clustering (mapping cells to reference by Seurat)
  • feat: support dataset with scRNA-seq data only (no scTCR-seq data)
  • feat: support diffusion map calculation (by ModuleScoreCalculator)
  • feat: support subclassing to cluster subsets of cells (by SeuratSubClustering)
  • feat: allow to ignore TCR data in TCellSelection and pass kmeans arguments
  • feat: allow to set multiple resolutions (envs.FindClusters.resolution) in SeuratClustering/SeuratClusteringOfTCells
  • change: change unsuperved cluster labels to c1, c2, ... in SeuratClustering by default
  • docs: add gallery, which contains real-world examples of datasets from publications

Breaking changes

  • change: rename SeuratMetadataMutater to IntegratingTCR
  • change: rename SeuratClusteringOfTCells to SeuratClustering
  • change: rename TCRClusters2Seurat to IntegratingTCRClusters
  • refactor: make SeuratClustering (instead of SeuratClusteringOfAllCells) work for all cells when all are T cells
  • change: move data preparation and integration from SeuratClustering to SeuratPreparing
  • change: default mode of ImmunarchLoading to paired (instead of single), which requires both alpha and beta chains (instead of beta chain only) to define a clonotype
  • change: default dbs for enrichment analysis wherever applies to KEGG_2021_Human and MSigDB_Hallmark_2020

Changes

  • feat: make TopExpressingGenes optional
  • feat: add validate_config to validate configuration schematically

Features

  • feat(SeuratPreparing): allow to filter genes directly (by specifying envs.gene_qc.excludes)
  • feat(SeuratClusterStats): add ngenes to plot the number of genes expressed in each cluster
  • feat(SeuratClusterStats): add barplot for features and allow aggregation of features
  • feat(SeuratClusterStats): add envs.mutaters to mutate meta data
  • feat(SeuratClusterStats): add histograms to plot number of cells against another variable
  • feat(SeuratClusterStats): Add frac_ofall and transpose for stats to calculate fraction within group or against all cells, and transpose ident and group, respectively

Dependencies

  • deps: add r-presto to conda environment files to support using presto to fastly find markers
  • deps: add bioconductor-destiny to conda environment file to support add diffusion map components in ModuleScoreCalculator
  • deps: add r-harmony to support harmony integration by Seurat v5 in conda env file
  • deps: add r-sf to conda env file
  • deps: remove vdjtools from conda env files
  • deps: bump pipen-report to 0.16.3
  • deps: bump biopipen to 0.23.3. Hightlight changes:
  • scrna.MarkersFinder: Add envs.use_presto to use presto to speed up finding markers
  • scrna.SeuratPreparing: Set envs.gene_qc.min_cells to 0 by default (instead of 3)
  • scrna.ScFGSEA: Allow to ignore small group when fgsea fails due to all NAs for pre-ranks
  • scrna.CellsDistribution: Allow to order clusters by envs.cluster_orderby
  • scrna.CellsDistribution: Add heatmaps
  • tcr.CloneResidency: Make section works in report
  • tcr.Immunarch: Support paired chain data for VJ conjuction plots
  • tcr.TESSA: Change envs.assay to None to use default assay of Seurat object
  • scrna.SeuratClusterStats: Add avgheatmap to plot more elegant heatmap for average gene expressions
  • scrna.SeuratClusterStats: Fix ident not working for dimplots
  • scrna.SeuratClusterStats: Add cluster_orderby to order clusters for features
  • scrna.SeuratClusterStats: Add na_group to keep NA values in group-by
  • utils.mutate_helpers: Change arguments id_col and compare_col of paired to id and compare, respectively
  • utils.mutate_helpers: Fix that subset can't be an expression for expanded family
  • utils.mutate_helpers: Add top to select top entities (e.g clones)
  • scrna.RadarPlots: Add breakdown and test to break down the cell distribution and run statistic test on the fractions

0.11.2

  • docs: move Immunarch to the later position in process list
  • docs: Use master tag in getting-started

0.11.1

  • chore: change line length to 88 for flake8
  • chore: dismissing warning about wasting columns for SeuratClusteringOfTCells
  • docs: update CHANGELOG.md with missing changes of last version
  • docs: add version of renaming envs.tcell_indicator to envs.tcell_selector
  • docs: remove unused doc files
  • docs: add metadata illustration
  • deps: bump biopipen to 0.22.8. Highlights:
  • deps: bump pipen-board to 0.13.10 (pipen-report to 0.16.2)
  • CellsDistribution: Don't add rownames to the output table file
  • MarkersFinder (ClusterMarkers/ClusterMarkersOfAllCells): Optimize to use FindAllMarkers if ident.1 is not specified
  • SeuratClusterStats: Fix path of expression table file
  • CellTypeAnnotation: Allow using NA to exclude clusters from output Seurat object
  • utils.mutate_helpers: Return ids only when subset is true and group is not NA for uniq = TRUE in expanded, collapsed, emerged and vanished

0.11.0

  • deps: update biopipen to 0.22.1, highlights:
  • add V-J junction circos plots to Immunarch process
  • add cache option to cache the clustering results if nothing changed except ncores, to SeuratClustering process
  • add dot plots to MarkersFinder (ClusterMarkersOfAllCells, ClusterMarkers) process
  • save exported table with only necessary columns for CellsDistribution process
  • add descr to describe cases cases in report for CellsDistribution process
  • add subset for dimplots in SeuratClusterStats process
  • use a new palette (biopipen) for related processes
  • optimize report rendering (using render_job() filter from pipen-report)
  • change metacols to extracols so essential columns get exported for ImmunarchLoading process
  • add cache option to cache the clustering results if nothing changed except ncores for SeuratClustering (SeuratClusteringOfAllCells) process
  • see more at https://github.com/pwwang/biopipen/releases/tag/0.22.0 and https://github.com/pwwang/biopipen/releases/tag/0.22.1
  • deps: update pipen-report to 0.16, highlights:
  • scroll anchor into view on the page
  • build report page when each process is done, instead of the whole pipeline
  • see more at https://github.com/pwwang/pipen-report/releases/tag/0.16.0
  • change: remove Immunarch2VDJtools and VJUsage processes (vj usage analysis can be done in Immunarch process)
  • change: change tcell_indicator to tcell_selector in TCellSelection process
  • enhance: provide better error message when none barcode matches from RNA and TCR data for TCRClustering process
  • docs: add memory usage reduction tips in FAQ
  • chore: dismiss warnings of wasted input columns for multiple processes

0.10.1

  • chore: update pipeline description to include version in the logs
  • fix: add fc-cache command to Dockerfile to solve Fontconfig error
  • docker: optimize building full image based off the base image

0.10.0

  • docker: lock r-matrix version to 1.6_1 for compatibility
  • docs: adopt mkdocs-rtd 0.0.10 (add scrollbar to the table of contents)
  • deps: bump biopipen to 0.21.1
  • use r-logger for logging in R scripts
  • docs: fix internal references in API docs
  • deps: bump pipen-board to 0.13.6
  • SampleInfo: refactor data subset logic using subset instead of distinct
  • Immunarch: add in.metafile to allow other meta info (i.e. seurat clusters) for future subsetting (#22)
  • Immunarch: fix empty groups in diversity plot after subsetting
  • Immunarch: allow subset to subset cells for analyses
  • Immunarch: allow separate_by also works on other diversity plots
  • Immunarch: add ymin and ymax to align diversity plots by separate_by
  • Immunarch: add ncol to specify # columns in the combined plots
  • RadarPlots: fix envs.order not working
  • MarkersFinder: add overlap to find overlapping markers between cases (#24)
  • MarkersFinder: allow subset to subset cells for analyses
  • MarkersFinder: add dot plots for significant markers
  • CellsDistribution: allow multiple columns for cells_by
  • CellsDistribution: allow subset to subset cells for analyses
  • utils.mutate_helpers.R: add include_emerged for expanded() and include_vanished for collapsed()

0.9.3

  • deps: Bump biopipen to 0.20.7
  • deps: Bump pipen-board to 0.13.4
  • ClusterMarkers/ClusterMarkersOfAllCells: Choose avg_log2FC > 0 markers by default
  • MarkersFinder: Allow to set assay and set assay to RNA by default
  • CellsDistribution: Add venn/upset plot for overlapping cell groups in different cases
  • SampleInfo: Add distinct to case to perform stats on distinct records

0.9.2

  • ➕ Add r-ggnewscale as dependency for CDR3AAPhyschem in docker image
  • ⬆️ Bump biopipen to 0.20.5
  • 🧱 CloneResidency: Integrate RNA data to allow more flexible analysis (i.e. within specific seurat clusters)
  • 🏗️ CloneResidency: Rename envs.sample_groups to envs.section to be consistent with other processes
  • 📝 ScFGSEA: Remove the link in the summary of the docstring (since they are not transformed in the report)
  • 🎨 CDR3AAPhyschem: Give better error message when wrong group items are given
  • ⬆️ Bump pipen-board to 0.13.3
  • Add items automatically when blurred for list options
  • Add other sections to description on the UI for processes

0.9.1

  • 🐛 Fix docstring for RadarPlots
  • ➕ Add pipen-diagram as dependency
  • ➕ Set pipen-runinfo as optional
  • ⬆️ Bump biopipen to 0.20.4
  • 📝 Update version in docs

0.9.0

Housekeeping and docs

  • Bump biopipen to 0.20.3 (pipen to 0.12)
  • Use pipen-cli-ref to generate API for processes (it uses docstring of the process class so that we don't need to maintain two copies of docs)

Fixed/Enhanced

  • Make /data directory in container, so it can be mounted
  • Fix a bug when a single gene provided to indicator_genes in TCellSelection
  • Move ModuleScoreCalculator before clustering so that the scores can be used in vars.to.regress of SCTransform while clustering
  • Set default assay to RNA in case module scores only caculated using integrated features in ModuleScoreCalculator
  • Improve QC plots in SeuratPreparing by marking the cells that are removed in the plots instead of doing before/after plots
  • Fix type annotation for envs.features_defaults.ncol in docstring for SeuratPreparing (causing pipen-board not converting to int)
  • Fix the cluster order in pie charts for CellsDistribution
  • Fix the cluster order in pie charts for SeuratClusterStats
  • Fix order in pie charts for SampleInfo
  • Fix docstring for envs.div.args of Immunarch (more clear description of method)
  • Allow mutiple columns in the file for envs.features_defaults.features in SeuratClusterStats
  • Allow order to be optional for CloneResidency (errored when not provided)
  • Add number of clusters at the end of log for SeuratClusteringOfAllCells/SeuratClusteringOfTCells
  • Add stricter checker for input file (#13)
  • Indicate the case name in logs when pie is enabled for group-by in SeuratClusterStats
  • Allow to skip overlap and gene usage analyses by setting method to none for Immunoarch (#11, #12)
  • Don't cluster on heatmap when there are only 2 samples for TCRClusterStats (#11)
  • Import Seurat explictly to avoid satijalab/seurat#2853 in MetabolicFeatures
  • Fix when NA values in data for heatmap in MetabolicPathwayActivity
  • Fix error when no significant pathways selected in MetabolicPathwayHeterogeneity
  • Give better error message in CellsDistribution if group value not found for CellsDistribution (#16)
  • Try including more genes (even though insignificant) in volcano plot for MarkersFinder/ClusterMarkers/ClusterMarkersOfAllCells (#17)
  • Add margins to volcano plot for MarkersFinder/ClusterMarkers/ClusterMarkersOfAllCells
  • Fix when envs.cell_qc is None (not provided) for SeuratPreparing
  • Fix ident in cases of envs.dimplots not working for SeuratClusterStats

Added

  • Add ClusterMarkersOfAllCells and TopExpressingGenesOfAllCells and set them as optional
  • Add dim plots in SeuratClusterStats to overlay TCR presence/absence of cells (#14)

Breaking changes

  • Rename TCRClusteringStats to TCRClusterStats (#15)

0.8.3

  • 📝 Fix typos in docs
  • 📝 Add links to some optional input files (#9, 5)
  • 🔨 Add apptainer to docker entry.sh (#9, 6)
  • 💄 Adjust process order in reports (#9, 1)
  • ⬆️ Bump pipen-report to 0.13.1 (#9, 2)

0.8.2

  • Bump biopipen to 0.18.3 to fix when either ident is empty for MarkersFinder

0.8.1

  • Bump biopipen to 0.18.2 to fix a bug when the min length of CDR3 seqs > 12 for CDR3AAphyschem

0.8.0

Housekeeping and docs updates

  • Bump biopipen to 0.18.1
  • Mention function changes with versions in docs
  • Add apptainer in board.toml so the command can be generated in pipen-board
  • Make logo shorter in docs
  • Add docker image with -full tags to include all dependencies
  • Print command help message if run test failed in CI
  • Add singularity/apptainer in FAQ for "no space left" question
  • Add -w fro apptainer in docs (as we need to save pipen-board file in home directory)

Added

  • Add TESSA process for tessa analysis
  • Add volcano plot for MarkersFinder and ClusterMarkers

Fixed

  • Fix when Sample is the only column in meta for ImmunarchLoading
  • Add clear message when k.weight is too large for IntegrateData in SeuratClustering
  • Allow unique: prefix for on in SampleInfo
  • Fix sample order in plots for SampleInfo
  • Remove tidyseurat:: prefix for filter in scripts of MetaMarkers, ScFGSEA and SeuratClusterStats in case tidyseurat::filter is not exported when installed from conda (but it will make dplyr::filter work anyway on seurat object)

Breaking changes

  • Redesign envs for SeuratClusteringStats to allow setting defaults for cases and switch identities for plots

0.7.0

Housekeeping and docs updates

  • Fix typos in docs/configurations
  • TCRClustering should be TCRClusteringStats in Multi-case variable design section
  • infile of [SampleInfo.in] should be samples.txt rather than sample.txt
  • Remove unused scripts by deprecated processes
  • Bump pipen-report to 0.12.8
  • Add master branch and master tag as stable tag for docker image
  • Add pdf version of the flowchart (#4)
  • Add warning for the results in getting started tutorial
  • Bump pipen-board to 0.11.5
  • Add apptainer to the docs

Added

Fixed

  • Fix default height and width for plots in SeuratClusterStats
  • Fix cluster order not kept after annotation using hitype in CellTypeAnnotation

Breaking changes

  • Change seurat_clusters_old to seurat_clusters_id to save old seurat_clusters in CellTypeAnnotation
  • Remove MarkersForClustersOfAllCells and TopExpressingGenesOfAllCells processes
  • Rename MarkersForClustersOfTCells to ClusterMarkers
  • Rename TopExpressingGenesOfTCells to TopExpressingGenes
  • Rename envs.exprs to envs.features for SeuratClusterStats
  • envs.exprs.genes is also renamed to envs.features.features

0.6.0

  • ⬆️ Bump biopipen to 0.16
  • 📝 Add documentation
  • 💚 Fix docs building in CI
  • 📝 Update README with flowchart

0.5.1

  • ✨ Add TopExpressingGenes
  • 🎨 Move RadarPlots to biopipen
  • ⬆️ Bump biopipen to 0.15.2

0.5.0

  • ⬆️ Upgrade biopipen to 0.15.0
  • 💚 Use better strategy docker image building

0.4.0

  • ⬆️ Bump biopipen to 0.6
  • ⬆️ Upgrade other dependencies
  • 💚 Use micromamba for docker image building
  • ⬆️ Add procps-ng for vdjtools for docker building

0.3.0

  • 💚 Use build 2 for genomeinfodbdata from bioconda (0.2.4)
  • 👽️ Use config from pipen_args
  • ⬆️ Pump biopipen to 0.5.3, pipen-args to 0.3.2
  • ⬆️ Upgrade deps for docker
  • 📝 Add flowchart in README.md
  • 🐛 Fix error when --config not passed

0.2.4

  • 💚 Use lastest miniconda3 for docker build
  • 💚 Use conda channel pwwang for bioconductor-genomeinfodbdata for fix (bioconda/bioconda-recipes#31349)
  • ⬆️ Upgrade biopipen to 0.4.9
  • 📝 Add URL to example in README

0.2.3

  • ⬆️ Upgrade biopipen to 0.4.8

0.2.2

  • ⬆️ Upgrade biopipen to 0.4.7 to fix SeuratPreparing

0.2.1

  • 🔥 Fix the bug of the wrong arguments in help page
  • ⬆️ Upgrade clustcr to 1.0.2
  • 📝 Fix docs for metabolic analysis

0.2.0

  • ♻️ Move in-house processes out of processes.py
  • ♻️ Split up MARKERS_FINDER
  • ♻️ Refactor RadarPlots
  • ✨ Add an example config file
  • ⚡️ Add filter for RadarPlots
  • 📝 Update docs
  • ⬆️ Upgrade deps
  • 🔧 Update docker/environment.yml
  • 🐛 Fix CloneHeterogeneity when only 1 row in continency table

0.1.1

  • 💚 Try fix pip in environment.yml
  • 📝 Update readme for requirement checking
  • 📝 Update docs to fix #1
  • 📝 Update CHANGELOG
  • ⬆️ Adopt biopipen 0.4.0

0.1.0

  • 🩹 Disable force-caching for some procs
  • ⬆️ Upgrade datar to 0.8.*
  • ✨ Add dockerfile
  • ⬆️ Upgrade pipen to 0.3
  • 💥 Remove gene lists from start processes
  • ⬆️ Upgrade biopipen to 0.3
  • ⬆️ Upgrade pipen to 0.3.5

0.0.7

  • Add CloneHeterogeneity
  • Allow setting indicator_gene for TCellSelection
  • Adopt latest datar and biopipen

0.0.6

  • ✨ Allow dimplots with clonal information

0.0.5

  • ✨ Allow more flexible dim plots

0.0.4

  • ✨ Refactor markers finder module and add meta-marker analysis

0.0.3

-✨ Add metabolic pathway analysis

0.0.2

  • Adopt biopipen 0.1.3

0.0.1

  • First release