Tag: H5AD

Obs_name 0 Can someone please help explain what the Obs_name represents? I exported the anndata matrix (h5ad) and attempted to transform it to the Seurat object using something similar to the following: exprs <- t(adata$X) colnames(exprs) <- adata$obs_names$to_list() rownames(exprs) <- adata$var_names$to_list() # Create the Seurat object seurat <- CreateSeuratObject(exprs) #…

Best compression for single cell RNA-seq object 0 I generated a scRNA-seq object (counts, PCA, UMAP embeddings, DEGs etc.) in Scanpy or Seurat. What is the best data structure to store this in to reduce the size of the object? I’m considering H5AD (scanpy/anndata), RDS or H5Seurat (Seurat), or Loom…