gravatar for jrleary

2 hours ago by

Lineberger Comprehensive Cancer Center

Pretty simple question; when I generate the counts matrix for my scRNAseq data using cellranger and read the object into R, the rows are genes and the columns are cells. However I've seen recently that algorithms such as PHATE expect rows to be cells and columns to be genes. Is this actually an important distinction for dimension reduction and clustering, and if so, which algorithms expect the initial count matrix to be transposed?

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