3 Data Ingress and Object Interoperability

This is the entry mainline of the package. Before users think about integration, annotation, or trajectory, they first need to bring data into sclet cleanly and keep it portable across ecosystems.

sclet is intentionally centered on SingleCellExperiment, but real projects rarely stay inside a single framework forever. This chapter therefore treats file import, object conversion, and recommended object semantics as one coherent starting route rather than a scattered set of utility helpers.

3.1 Seurat and SCE Conversion

sclet provides simple conversion helpers between Seurat and SCE objects.

library(sclet)

# SCE to Seurat
# seurat_obj <- as.Seurat(sce_obj)

# Seurat to SCE
# sce_obj <- as.SCE(seurat_obj)

3.2 AnnData (h5ad)

Python’s AnnData format (.h5ad) is widely used. sclet uses zellkonverter-based helpers to provide easy read/write functions.

# Read h5ad
# sce <- ReadH5AD("path/to/data.h5ad")

# Write h5ad
# WriteH5AD(sce, "path/to/output.h5ad")

This allows you to easily move data between R and Python environments, leveraging the best tools from both ecosystems (e.g. sclet/Bioconductor in R and scanpy in Python).