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A set of scripts for running Expression-Weighted Cell-type Estimation (EWCE)
Well hello there, I just stumbled upon this repo. I actually just made a pull request to EWCE to add a number of useful features, including "ingest_data" which can take in scRNAseq data from any species and standardize it as SingleCellExperiment. EWCE can now take these SCE objects from pretty much any format (matrix + colData, loom, Seurat, h5, anndata, etc.) and turn them into CTD refs. It also uses DelayedArray which is enables processing of arbitrarily large datasets by only reading in one chunk at a time (across cores).
I'm using these new features to generate a bunch of new refs, including from the latest Linnaerson development mouse brain atlas: http://mousebrain.org/
I'm creating multiple levels of annotation including cell-type, cell type by region, and cell-type by developmental age.
If this is something that might be useful let me know and I can pass it along once it's ready!
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