Install using devtools
devtools::install_github("jakeyeung/AnnotateCelltypes", ref = "main")
Check out in the vignette load_reference_infer_celltype_from_raw.R for an example of how to load prob mat and raw count mat and output inferred celltypes.
load_reference_infer_celltype_from_raw.R can be run on commandline:
Rscript load_reference_infer_celltype_from_raw.R -inraw $INRAW -inref $INREF -outdir $OUTDIR
The vignette annotate_celltype_setup_example.r is an example of how to create the probability matrix and also testing that this probability matrix works for annotate new cells from raw counts.
See inst/extdata for example input files