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)