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waldronlab / SingleCellMultiModal

Single Cell multimodal data scripts for downloading datasets
https://bioconductor.org/packages/SingleCellMultiModal
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celltype annotations #51

Closed drighelli closed 1 year ago

drighelli commented 1 year ago

It seems that we have some already annotated datasets, such as: 

SCNMT mouse gastrulation: column lineage
10X multiome: column celltype
seqFISH: both RNAseq and seqFISH (column class)
SCOPE2: protein part column celltype

on the other hand annotation is missing for:

CITE-seq and ECCITE-seq -> self assigned
GNTseq: Ludwig could you please check about the original paper annotations for this data type, we can discuss it in this thread. :)

@lgeistlinger

lgeistlinger commented 1 year ago

Hi @drighelli - sorry for the delay! I've checked the G&T papers and it seems that there are no cell type labels available for the Mouse embryo dataset. Do you intend to annotate them computationally eg based on their scRNA-seq profile? This might be a bit of a far shot given that this annotation is not provided by the authors.

drighelli commented 1 year ago

Thanks @lgeistlinger, I don't think it's a good idea to assign cell labels to the dataset by ourselves, in particular if we want to define a ground truth.

drighelli commented 1 year ago

we reported the already existing cell types and annotated the CITEseq dataset with a manual gating. We also exported two functions for manual gating getCellGroups and addCTlabels, an example of usage can be seen in the scripts/CITEseq_celltypes.R file