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Create signature matrix with average_clusters() using bulkRNAseq data #397
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Thanks for your interest in the package:
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hello,
I am trying to create a cell-type signature matrix from bulkRNAseq of FACS sorted mono-cell-types samples:
whereby the columns represent samples (different patient samples) and rows are annotated GrCh38 gene names.
expr_matrix
is derived from raw counts, after alignment to GRch38 using the standard nf-core/RNAseq pipeline, and then normalised usingvarianceStabilizingTransformation()
in DESeq2I understand that in Clustifyr the best approach would be to use
average_clusters()
(?)But then I am unsure if:
average_clusters()
correctly ?new_ref_matrix
?new_ref_matrix
with other reference signature matrices derived from single cell data?Any advice, insights or lead to helpful material will be very much appreciated
Thanks all
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