I have been provided with the gene expression matrices produced by spaceranger (matrix, feature and barcodes) and also the lower res images generated by spaceranger and the image alignment information (the spatial folder). However I do not have the h5 file generated to be loaded in Load10X function for the analysis. Do you know any way I can load these data for the analysis of Spatial Transcriptomics?
I have read this previous post (Spatial transcriptomics data). I have tried to generate a h5 file with the rhdf5, but when I try to write in the h5 file the matrix I have the following error:
Error in UseMethod("h5writeDataset") : no applicable method for 'h5writeDataset' applied to an object of class "c('dgTMatrix', 'TsparseMatrix', 'dsparseMatrix', 'generalMatrix', 'dMatrix', 'sparseMatrix', 'compMatrix', 'Matrix', 'xMatrix', 'mMatrix', 'replValueSp')"
Any idea about how to proceed?. Is the h5 file needed for the Spatial using the Satija lab tutorial?