R/Python conversion

Instructions to read h5ad file in R: We provide Python and R scripts to convert a Python h5ad file into an R Seurat file. Please download the h5ad file of interest and Python script “LCA_h5ad2csv.py” to the same folder, and run in Python << python LCA_h5ad2csv.py -i input.h5ad -o output_folder -c layer_id >>, where input.h5ad is the h5ad file of interest, output_folder is the folder where the csv files will be exported, and layer_id is the gene count matrix to export (if layer_id = raw_counts, then the raw data is exported (adata.layers[‘raw_counts’]); if layer_id = log, then the log transformed data is exported (adata.X)). Then run “LCA_csv2seurat.R” in R to create a Seurat object from the csv files.