Tag: H5AD

scRNAseq analysis – h5ad file conversion to Seurat format

scRNAseq analysis – h5ad file conversion to Seurat format 0 Hi all. I have a single .h5ad file that contains scRNAseq data from several samples. I would like to convert it so that I can open it in Seurat (I am comfortable with R, but not with Python). I have…

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Single cell database scrna dB for bioinformatics database development (1)

Single cell database construction High quality integrated single cell database If readers just want to get a ready-made single-cell database with rich content and add it to their own PC or linux The server , You can skip the following detailed theoretical tutorial Database download link : Click to download…

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Obs_name

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) #…

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Best compression for single cell RNA-seq object

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…

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