convert_seurat_to_h5ad.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "6ec68ca4",
   "metadata": {},
   "outputs": [],
   "source": [
    "library(Seurat)\n",
    "library(SeuratDisk)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "8267e257",
   "metadata": {},
   "outputs": [],
   "source": [
    "library(Seurat)\n",
    "library(SeuratData)\n",
    "library(SeuratDisk)\n",
    "\n",
    "# Load the RDS file\n",
    "seurat_object <- readRDS(\"input.rds\")\n",
    "\n",
    "# Check the Seurat version\n",
    "if (\"Seurat\" %in% class(seurat_object)) {\n",
    "  print(seurat_object@version)\n",
    "} else {\n",
    "  print(\"The loaded object is not a Seurat object.\")\n",
    "}"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "155e058c",
   "metadata": {},
   "outputs": [],
   "source": [
    "SaveH5Seurat(seurat_object, filename = \"intermediate.h5Seurat\")\n",
    "Convert(\"intermediate.h5Seurat\", dest = \"h5ad\")"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "id": "81723928",
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "R",
   "language": "R",
   "name": "ir"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}

r_seuratdisk.yaml

name: r_seuratdisk_env
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - r-base
  - r-seuratdisk
  - r-seurat
  - r-irkernel  # For Jupyter integration
  - nb_conda_kernels