carmonalab/ProjecTILs: ProjecTILs v3.5.0

New in this version:

• Address compatibility with Seurat v5 assays. When query objects have multiple layers, they are automatically joined. While most compatibility issues should be solved, we do recommend, when possible, to work with single layers (see Seurat::JoinLayers()) and to set options(Seurat.object.assay.version = "v3") for ProjecTILs analyses.
• New function get.reference.maps() to retrieve collections of reference maps. Used for multi-atlas classification by HiTME.
• New parameter 'overwrite' for ProjecTILs classifier, enabling sequential classification using multiple references.
• New function FindAllMarkers.bygroup(), to extract DEGs that are consistently significant across multiple samples. Useful to identify cell type markers that are conserved across samples/datasets.
• New function celltype.heatmap(), to calculate and plot pseudo-bulk gene expression by cell type and custom grouping variables. Data can be split in principle by any metadata present in the starting Seurat object (e.g. patient, tissue, study, etc.). This can be useful to evaluate consistency of expression profiles for different cell types across samples, studies or other grouping variables.
• Use internal neighbor consistency to calculate consistency score for predicted labels; return NA for low confidence labels (with threshold determined by min.confidence.score())
• Include checksum to verify complete download of reference maps.
• Autodetect OS and redirect BiocParallel to MultiCore, Snow or Serial
• Update radar visuals, to account for changes to geom_radial in ggplot2 version 3.5.0