Immunopipe

- 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/biopipen112)

- 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`

- 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/biopipen113)
- 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`

- 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

- 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

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](https://github.com/pwwang/pipen-report/releases/tag/0.16.3)
- deps: bump `biopipen` to [0.23.3](https://github.com/pwwang/biopipen/releases). 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