Format
h5ad (AnnData)
AnnData on disk: X, layers, obs, var, obsm, uns. Cells are rows, genes are columns, the transpose of the R convention.
Extensions: .h5ad · Coordinates: n/a · Specification
From h5ad (AnnData)
- How to Convert h5ad to SingleCellExperiment (Without Losing Your Metadata)
readH5AD does the transpose and slot mapping for you, but obs metadata and uns objects can survive broken or vanish silently, so check before you trust the object.
- How to Convert h5ad to Seurat object (Without Losing Your Metadata)
anndataR and capseuratconverter handle the transpose and slot mapping for you; deciding which layer actually becomes your counts slot is still on you.
To h5ad (AnnData)
- How to Convert 10x HDF5 to h5ad (and Why IDs Go Missing)
read_10x_h5 looks like a one-line import, but its two default arguments quietly decide which features and which gene identifiers survive into your AnnData object.
- How to Convert 10x MTX to h5ad (and Why IDs Go Missing)
The default read call quietly swaps your Ensembl IDs for gene symbols, and the duplicate-name patch that follows hides the damage instead of fixing it.
- How to Convert SingleCellExperiment to h5ad (Without Losing Your Metadata)
writeH5AD() decides which assay becomes X almost silently, get that wrong and every downstream scanpy step runs on the wrong matrix.
- How to Convert Seurat object to h5ad (Without Losing Your Metadata)
Seurat v5's split layers and multiple assays don't collapse into a single AnnData X on their own; pick the assay and layer yourself or the converter will guess wrong.