biopipen

A set of processes/pipelines for bioinformatics

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biopipen - 0.23.4

Published by pwwang 10 months ago

  • 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

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.3...0.23.4

biopipen - 0.23.3

Published by pwwang 10 months ago

  • tcr.ImmunarchLoading: change mode from single to paired by default

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.2...0.23.3

biopipen - 0.23.2

Published by pwwang 10 months ago

  • scrna.RadarPlots: fix test error when not enough observations
  • scrna.RadarPlots: add n and mean to test table

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.1...0.23.2

biopipen - 0.23.1

Published by pwwang 10 months ago

  • scrna.RadarPlots: fix error when generating report for tests when breakdown is not provided

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.23.0...0.23.1

biopipen - 0.23.0

Published by pwwang 10 months ago

  • deps: bump pipen to 0.12.5
  • deps: bump pipen-report to 0.16.3
  • deps: Update seurat to 5.0.1 in test env file
  • chore: Add /tmp to .gitignore
  • scrna.MarkersFinder: Add envs.use_presto to use presto to speed up finding markers
  • scrna.MarkersFinder: Fix a bug when subsetting cells
  • scrna.MarkersFinder: Set envs.dbs to KEGG_2021_Human and MSigDB_Hallmark_2020 by default
  • scrna.MarkersFinder: Fix FindAllMarkers/FindMarkers for SCTransform'ed data
  • scrna.SeuratPreparing: Fix handling of empty path in RNAData
  • scrna.SeuratPreparing: Set envs.gene_qc.min_cells to 0 by default (instead of 3)
  • scrna.SeuratPreparing: Add sample integration procedures
  • scrna.SeuratPreparing: Allow to filter genes directly
  • scrna.SeuratClustering: Add options to limit string and numeric output length to have more exact caching signature
  • scrna.SeuratClustering: Set default random.seed to 8525 for FindClusters
  • scrna.SeuratClustering: Allow multiple resolutions for FindClusters
  • scrna.SeuratClustering: Print table of idents in log for found clusters
  • scrna.SeuratClustering: Move integration procedues to SeuratPreparing and do only clustering
  • scrna.SeuratClustering: Update tests
  • scrna.SeuratClustering: Make the cluster labels start with "c1" instead of "0"
  • scrna.SeuratClustering: Default reduction of RunUMAP and FindNeighbors to pca
  • scrna.SeuratClustering: Fix test
  • scrna.SeuratClustering: Print less verbosal log
  • scrna.SeuratClusterStats: Add ngenes to plot the number of genes expressed
  • scrna.SeuratClusterStats: Add barplot for features and allow aggregation of features
  • scrna.SeuratClusterStats: Fix matching kind for plots of features
  • scrna.SeuratClusterStats: Use new umap for plotting feature and dimplots for sub-clustering
  • scrna.SeuratClusterStats: Use default assay for plotting of number of genes expressed
  • scrna.SeuratClusterStats: Add envs.mutaters to mutate meta data
  • scrna.SeuratClusterStats: Add histograms to plot number of cells against another variable
  • scrna.SeuratClusterStats: Fix reduction for subclustering for dimplots
  • scrna.SeuratClusterStats: Subset seurat object for featureplots when ident is subclusters
  • scrna.SeuratClusterStats: Fix argument layer not excluded for heatmaps in features
  • scrna.SeuratClusterStats: Add frac_ofall and transpose for stats to calculate fraction within group or against all cells, and transpose ident and group, respectively
  • scrna.ModuleScoreCalculator: Fix features not being passed to AddModuleScore as a list
  • scrna.ModuleScoreCalculator: Support calculating diffusion map components
  • scrna.SeuratMap2Ref: Rename envs.alias to `envs.name
  • scrna.SeuratMap2Ref: Set default value of envs.MappingScore.ndim to 30
  • scrna.SeuratMap2Ref: Add envs.ncores for parallelization
  • scrna.SeuratMap2Ref: Remove preset MapQuery arguments
  • scrna.SeuratMap2Ref: Raise an error when envs.MapQuery.refdata is not provided
  • scrna.SeuratMap2Ref: Default envs.use to the key of envs.MapQuery.refdata with single key
  • scrna.SeuratMap2Ref: Use layer instead of slot in docstring (Seurat v5)
  • scrna.SeuratMap2Ref: Make sure the column of cluster labels is a factor
  • scrna.ScFGSEA: Allow to ignore small group when fgsea fails due to all NAs for pre-ranks
  • scrna.ScFGSEA: Use default assay and use layer instead of slot (Seurat v5)
  • scrna.TopExpressingGenes: Use default assay of Seurat object and fix column names of average expression (Seurat v5)
  • scrna.TopExpressingGenes: Change default enrichment gene sets to KEGG_2021_Human and MSigDB_Hallmark_2020
  • scrna.MetaMarkers: Change default enrichment gene sets to KEGG_2021_Human and MSigDB_Hallmark_2020
  • scrna.MetaMarkers: Give better message when tests for genes fail
  • scrna.MetaMarkers: Give error message when not enough cells in case
  • scrna.CellsDistribution: Allow to order clusters by envs.cluster_orderby
  • scrna.CellsDistribution: Add heatmaps
  • scrna.SeuratSubClustering: Add process
  • scrna_metabolic_landscape: Add InlineNotification component to imports for report
  • scrna_metabolic_landscape.MetabolicFeatures: Fix when default assay is SCT
  • scrna_metabolic_landscape.MetabolicFeaturesIntraSubset: Fix when default assay is SCT
  • scrna_metabolic_landscape.MetabolicPathwayActivity: Fix when default assay is SCT
  • scrna_metabolic_landscape.MetabolicPathwayActivity: Use default assay of Seurat object
  • scrna_metabolic_landscape.MetabolicPathwayHeterogenetiy: Fix when default assay is SCT
  • scrna.CellTypeAnnotation: Use layer instead of slot of Seurat object (Seurat v5) for sctype
  • tcr.ImmunarchLoading: Allow empty path in TCRData column in input file
  • tcr.ImmunarchLoading: Do not hide envs.mode anymore in docs
  • tcr.CloneResidency: Fix stringifying the subject in case it is a factor
  • 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_basic: remove scrna_basic pipeline, use immunopipe instead
  • scrna.GeneExpressionInvestigation: Remove deprecated code
  • scrna.Write10X: Use layer instead of slot (Seurat v5)
  • scrna.ExprImputation: Use default assay of seurat object
  • scrna.SeuratTo10X: Rename Write10X to SeuratTo10X
  • scrna.SeuratSubClustering: Fix original reduction being poluted by subclustering
  • scrna.SeuratClusterStats: Add avgheatmap to plot more elegant heatmap for average gene expressions
  • scrna.SeuratClusterStats: Fix ident not working for dimplots
  • scrna.SeuratClusterStats: Fix for hists when x is a factor/character vector
  • scrna.SeuratClusterStats: Add cluster_orderby to order clusters for features
  • scrna.SeuratClusterStats: Add na_group to keep NA values in group-by
  • scrna.SeuratClusterStats: Allow avgheatmap to plot features other than gene expressions
  • scrna.SeuratClusterStats: Add mutate_helpers.R source file
  • scrna.SeuratClusterStats: Fix data binding for avgheatmap in features
  • utils.mutate_helpers: Change arguments id_col and compare_col 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

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.8...0.23.0

biopipen - 0.22.8

Published by pwwang 10 months ago

  • scrna_metabolic_landscape.MetabolicPathwayActivity: Fix useNames = NA being deprecated in matrixStats v1.2 (more locations)
  • scrna_metabolic_landscape.MetabolicPathwayActivity: Fix heatmap column_split
  • scrna_metabolic_landscape.MetabolicFeaturesIntraSubset: Sort groups when being processed
  • utils.gsea: Fix useNames = NA in rowSds for matrixStats v1.2
  • utils.mutate_helpers: Fix tests

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.7...0.22.8

biopipen - 0.22.7

Published by pwwang 10 months ago

  • scrna_metabolic_landscape.MetabolicPathwayActivity: Fix useNames = NA being deprecated in matrixStats v1.2

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.6...0.22.7

biopipen - 0.22.6

Published by pwwang 10 months ago

  • Bump pipen-board to 0.13.10 (pipen-report to 0.16.2)

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.5...0.22.6

biopipen - 0.22.5

Published by pwwang 10 months ago

  • docs: Bump pipen-board to 0.13.9 (pipen-report to 0.16.1)
  • cellranger.CellRangerCount: Update iframe height in report
  • cellranger.CellRangerVdj: Update iframe height in report

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.4...0.22.5

biopipen - 0.22.4

Published by pwwang 10 months ago

  • utils.mutate_helpers: Update docs

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.3...0.22.4

biopipen - 0.22.3

Published by pwwang 10 months ago

  • utils.mutate_helpers: Return ids only when subset is true and group is not NA for uniq = TRUE in expanded, collapsed, emerged and vanished

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.2...0.22.3

biopipen - 0.22.2

Published by pwwang 10 months ago

  • docs: Update logo and favicon
  • docs: Update logo height in README.md
  • core.filters: Add exclude argument to dict_to_cli_args filter
  • cellranger: Add CellRangerCount and CellRangerVdj
  • scrna.CellTypeAnnotation: Allow using NA to exclude clusters from output Seurat object
  • scrna.SeuratClusterStats: Fix path of expression table file
  • scrna.MarkersFinder: Use FindAllMarkers if ident.1 is not specified
  • scrna.CellsDistribution: Don't add rownames to the output table file
  • utils.mutate_helpers: Add debug and each to expanded, collapsed, vanished and emerged

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.1...0.22.2

biopipen - 0.22.1

Published by pwwang 10 months ago

  • scrna.CellsDistribution: Export table with distinct columns
  • scrna.SeuratMetadataMutater: Warn about existing columns in seurat object
  • tcr.ImmunarchLoading: Change metacols to extracols so essential columns get exported
  • tcr.Attach2Seurat: Detach prefix from template in code
  • tcr.CDR3AAPhyschem: Detach prefix from template in code
  • tcr.Immunarch: Use immdata$prefix as prefix by default
  • tcr.TCRClustering: Use immdata$prefix as prefix by default
  • tcr.TESSA: Allow in.immdata to be either an RDS file of immunarch object or a text file of cell-level expanded data

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.22.0...0.22.1

biopipen - 0.22.0

Published by pwwang 11 months ago

  • Bump pipen-board to 0.13.8 (pipen-report to 0.16)
  • Use render_job filter to generate report
  • utils: Add biopipen palette
  • scrna.SeuratClusterStats: Add subset for dimplots to
  • scrna.CellsDistribution: Add descr for cases in report
  • scrna.CellsDistribution: Save the table only with necessary columns
  • scrna.MarkersFinder: Add dot plot
  • scrna.MetaMarkers: Use logger to log messages
  • scrna.SeuratClustering: Use logger to log messages
  • scrna.SeuratClustering: Add cache option to cache the clustering results if nothing changed except ncores
  • delim.SampleInfo: Fix handling of null exclude_cols

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.21.2...0.22.0

biopipen - 0.21.2

Published by pwwang 11 months ago

  • tcr.Immunarch: Add V-J junction circos plots
  • tcr.Immunarch: Refactor logging statements using r-logger

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.21.1...0.21.2

biopipen - 0.21.1

Published by pwwang 11 months ago

  • deps: Update pipen-board and pygments versions
  • docs: Adopt mkdocs-rtd 0.0.10
  • docs: Fix internal reference in API docs
  • delim.SampleInfo: Refactor data subset logic in SampleInfo class

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.21.0...0.21.1

biopipen - 0.21.0

Published by pwwang 11 months ago

  • tcr.Immunarch: Fix empty groups in diversity plot after filtering
  • tcr.Immunarch: Add in.metafile to allow other meta info (i.e. seurat clusters) for future subsetting (pwwang/immunopipe#22)
  • tcr.Immunarch: Change envs.mutaters now on expanded (cell-level) data
  • tcr.Immunarch: Add subset for cases to do analysis on a subset of data
  • tcr.Immunarch: Add separate_by also works on other diversity plots
  • tcr.Immunarch: Add ymin and ymax to align diversity plots by separate_by
  • tcr.Immunarch: Add ncol to specify # columns in the combined plots
  • scrna.RadarPlots: Fix envs.order not working
  • scrna.MarkersFinder: Add overlap to find overlapping markers between cases (pwwang/immunopipe#24)
  • scrna.MarkersFinder: Add subset for each case to subset cells
  • scrna.MarkersFinder: Add dot plots for cases
  • scrna.CellsDistribution: Allow multiple columns for cells_by
  • scrna.CellsDistribution: Add subset for cases to subset cells
  • cnv.AneuploidyScoreSummary: Ignore .call suffix to get sample name by default
  • cnv.AneuploidyScoreSummary: Fix image path in report while envs.group_cols is a string (not an array)
  • utils.single_cell.R: Add functions to expand, filter and restore immunarch objects
  • utils.common_docstrs: Extract some common docstrings for procs
  • utils.misc.R: Use r-logger for logging for R scripts
  • utils.mutate_helpers.R: Add include_emerged for expanded() and include_vanished for collapsed()
  • utils.mutate_helpers.R: Fix tests
  • tests: Add r-logger to test dependencies

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.20.7...0.21.0

biopipen - 0.20.7

Published by pwwang 12 months ago

  • (delim.SampleInfo) Add distinct to case to perform stats on distinct records
  • (scrna_basic) Fix docker image building

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.20.6...0.20.7

biopipen - 0.20.6

Published by pwwang 12 months ago

  • ⬆️ Bump pipen-board to 0.13.4
  • ✨ [scrna.MarkersFinder] Allow to set assay for Seurat::FindMarkers()
  • ✨ [scrna.CellsDistribution] Add venn/upset plot for overlapping cell groups in different cases

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.20.5...0.20.6

biopipen - 0.20.5

Published by pwwang 12 months ago

  • ⬆️ Bump pipen-board to 0.13.3
  • 🏗️ [tcr.CloneResidency] Rename envs.sample_groups to envs.section to be consistent with other processes
  • 🏗️ [tcr.CloneResidency] Allow additional metadata from input for more flexible case definition (i.e. analysis for specific seurat clusters)
  • 📝 [scrna.ScFGSEA] Remove the link in the summary of the docstring (since they are not transformed in the report)
  • 🎨 [tcr.CDR3AAPhyschem] Give better error message when wrong group items are given

What's Changed

Full Changelog: https://github.com/pwwang/biopipen/compare/0.20.4...0.20.5

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