Convert your .rds to .h5ad
Upload a Seurat .rds object and download a converted AnnData .h5ad file. Use it with Python-based tools like Scanpy, scvi-tools, and CellRank, or submit to repositories like CELLxGENE Discover. All metadata is preserved — no R or Python installation required.
Upload your Seurat object
Drag & drop your .rds file here
or click to browse
Max file size: 100 MB
What gets preserved
- Expression matrices (raw counts and normalized data)
- Cell metadata (
@meta.data→.obs) - Gene metadata (
@meta.features→.var) - Dimensional reductions (PCA, UMAP, tSNE →
.obsm) - Nearest-neighbor graphs →
.obsp - Default assay layers (counts, data, scale.data) →
.layers - Unstructured metadata →
.uns
What doesn't get preserved
- Non-default assays — only the default assay (typically RNA) is converted. Additional assays like ADT or ATAC are not included, as AnnData does not have a native multi-assay structure
- Reductions from other assays — dimensional reductions associated with a non-default assay are skipped
- Spatial images —
@imagesslots from spatial Seurat objects have no AnnData equivalent - Command log —
@commands(the history of Seurat functions run) is not transferred
Looking to convert in the other direction? Convert .h5ad to .rds