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

ProjecTILs-3.0

ProjecTILs version 3.0

New in this version:

• new function make.reference for easy conversion of custom Seurat objects into reference maps for ProjecTILs. See custom map tutorial for an example (not T cells this time :))
• new function Run.ProjecTILs as a wrapper for projection (make.projection) and cell type prediction (cell.states.predict).
• new function ProjecTILs.classifier to transfer labels to query without altering the embeddings of the query dataset
• new split.by option in Run.ProjecTILs and ProjecTILs.classifier to split datasets by a grouping variable (normally the sample or the sequencing batch) before projection; results are then re-merged after projection into a single object.
• new function recalculate.embeddings to recompute PCA and/or UMAP after projection, accounting for both reference and query cells. This may be used as a way to update a reference when a query dataset contains a novel cell type / cell state.
• updates to the projection algorithm to use batch-effect correction as in STACAS-2.0. This includes anchor weighting based on rPCA distance, and STACAS.k.weight="max" by default, which disables local re-weighting of integration anchors.
• support for uwot for UMAP embeddings in new references generated with make.reference; the projection algorithm automatically detects which algorithm was used for reference building and applies the same method for query data embedding. NOTE: there are known issues with saving uwot models to .rds files (see e.g. this issue) - the default method in ProjecTILs remains umap until this issue is solved.
• allow plotting signature scores on radar plots. Set using meta4radar parameter in plot.states.radar function.
• keep specified order of genes in plot.states.radar (previously was automatically reordered alphabetically)
• exposing function merge.Seurat.embeddings (previously available as internal function): a utility function that merges two Seurat objects as well as their low dimensional embeddings
• allow specifying a custom list of genes to find.discriminant.genes, e.g. to exclude pseudo-genes or ribosomal genes from DEG analysis

ProjecTILs-2.0

ProjecTILs version 2.0

New in this version:

• Allow reference atlases to be for mouse or human, and for any cell type. See for example APC reference
• Automatic pre-filtering of cell types represented in the atlas using scGate. This replaces the automatic filtering by TILPRED. Atlas objects should contain a scGate model in the slot ref@misc$scGate, otherwise a default T cell filter is applied.
• Cell cycling scores are now calculated using UCell and the signatures from Tirosh et al. (2016) for the G1/S and G2/M phases.
• Remove dependency from TILPRED
• Implement fast.mode option for projection, which by-passes umap::umap.predict. This is faster and allows using reference atlases built with other methods than the umap package.
• Fix some issues with meta.data classes, and remove 'Q_' prefix from barcodes of projected cells, as documented in issue #17
• More flexible implementation for reading 10x files
• Update table of mouse-human orthologs to include some genes that were missing (e.g. Lamp3 = LAMP3; H2-Aa = HLA-DQA)

ProjecTILs v1.0.0

New in version 1.0.0:

• Speed up execution time by parallelizing projection of multiple samples (requires future.apply)
• Auto-detection of human or mouse data. Option human.ortho is now deprecated
• Read color palette stored with atlas object, if available
• Improved handling of separators for raw matrix formats in read.sc.query function

Zenodo publication

Update functions.md

add find.discriminant.genes

New features for v0.6.0

• Implements differential expression analysis on specific cell states
• Try/catch for projecting a list of objects
• Internal merge function that preserves embeddings
• Improved error handing

Stable release compatible with Seurat >3.2.1

v0.5.1

Update README.md

Support for human ortholog projection

This release includes support for R version 4.0+, and implements projection of human data on mouse atlases (human.ortho=TRUE)

First production release, compatible with R version 3.6.1

v0.2.4

Update README.md