carmonalab/ProjecTILs: ProjecTILs-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)