Format
SingleCellExperiment (RDS)
Bioconductor's single-cell container with assays, colData, rowData and reducedDims; genes are rows.
Extensions: .rds · Coordinates: n/a · Specification
From SingleCellExperiment (RDS)
- 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 SingleCellExperiment to Seurat object (Without Losing Your Metadata)
as.Seurat() copies your matrices and cell metadata fine; it quietly leaves your gene annotations and altExps behind.
To SingleCellExperiment (RDS)
- 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 Seurat object to SingleCellExperiment (Without Losing Your Metadata)
as.SingleCellExperiment() is one line, but that line decides which assay becomes primary, drops your scaled matrix, and can hand back an empty counts assay without ever throwing an error.