Closed MaximilianNuber closed 9 months ago
Hi @MaximilianNuber
Thanks for your interest in using CellScopes. I tried the MCA 400K dataset again today, and the cs.scRNAObject
took about 5 seconds. It shouldn't be that long. Here are some thoughts:
@time rawcount = cs.RawCountObject(counts, cells, genes);
obs.UMIs needs to be a vector of cell ids.
typeof(counts)
it should be SparseMatrixCSC{Int64, Int64}
. If not, please convert it to that type.
Let me know if those steps don't help.
Dear @HaojiaWu,
Please forgive my late reply. Yes, it was about the type of the CSC matrix, which was of LinearAlgebra.Transpose(CSC matrix...
, because I needed to transpose the matrix after saving it from scanpy. Converting to CSC matrix or just copy()
worked both.
Thank you and apologies again for my late reply.
Best, Max
Hello everyone,
Thank you for the great package, I am looking forward to working with CellScopes and Julia more (MLE Mixed models being absent in Python to my knowledge and my data being too large for R :P).
I have an issue constructing the scRNAObject. The function does not finish after hours, even when running over night. previously I constructed the Raw count object from a sparse matrix, gene_names and cell_names.
I am working with a dataset of 380k cells that I preprocessed and annotated in Python. I saved the counts matrix (thats why I had to transpose, coming from scanpy) and gene and cell annotations. When loading/converting from .h5ad I had the same issue of the function never ending.
adata = cs.from_scanpy("scVI-integrated.h5ad"; data_type="scRNA", anno="cell_type")
Looking at the 400k cell tutorial, it seemed like creating the object should be quite fast.
Did I forget about something?
(Julia 1.8.1, only installed Gadfly, removed Gadfly, install MatrixMarket, CSV, DataFrames and SingleCellProjection, in addition to CellScopes. Am quite new to Julia).
Thank you for any help :)