Create single cell reference for MuSIC

Question

[FrankStarling]

I am attempting to use MuSIC to deconvolve bulk data from various kidney cell types. I have read the documentation yet still have a remaining question. The single nuclei data i am trying to use as a refernce is found here(https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE131685).

The files included are kidney_barcodes.tsv, kidney_features.tsv, and kidney_matrix.mtx. I have browsed the files by importing into r. From my understanding I need a matrix where rows are genes and columns are cells(or nuclei in this case).

Thus my question is how do I (or can I) go about constructing this matrix from the downloaded data? This is my first go at deconvolution so please let me know if I am completely mistaken.

Answer 1

[rpolicastro]

According to their github they support SingleCellExperiment objects as input (>= v1.0.0). Assuming your three 10X files are formatted correctly you can put them into a directory and read them into a SingleCellExperiment in R by using the read10XCounts function from DropletUtils.

[FrankStarling]

Thank you for the response. It seems DropletUtils is what I was looking for.