I have single cell mRNA expression matrix in a CSV file, how can I save it as AnnData (H5ad) format? I can export to the h5 format using pandas, yet it's not optimized for scRNA and support is lacking in many scRNA tools
I converted the count matrix to seurat object (using seurat package) and then to h5ad. Library used is sceasy. However, it requires reticulate package. Configuration is little bit tricky. Once configured, code is straight forward convertFormat(smdf2, from="seurat", to="anndata",outFile="test.h5ad"). If you are using Matrix package, load reticulate package just before conversion.