Seurat转换为H5AD

参考链接：https://mp.weixin.qq.com/s/unwfRqWGjJYu9wXwaZwu7Q

1. srtdisk

github链接：https://github.com/mianaz/srtdisk
国内大佬修改SeuratDisk后的包，使用同SeuratDisk

Installation

if (!requireNamespace("remotes", quietly = TRUE)) {
  install.packages("remotes")
}
remotes::install_github("miana/seuratdisk-v5")

Seurat to AnnData (h5ad)

library(Seurat)
library(srtdisk) # changed package name

# Save Seurat object as h5Seurat
SaveH5Seurat(seurat_obj, filename = "data.h5Seurat")

# Convert to h5ad for Python/Scanpy
Convert("data.h5Seurat", dest = "h5ad")

AnnData to Seurat

# Convert h5ad to h5Seurat
Convert("data.h5ad", dest = "h5seurat")

# Load as Seurat object
seurat_obj <- LoadH5Seurat("data.h5seurat")

Spatial Visium Data

# Load Visium data from h5ad (created with Scanpy/Squidpy)
brain <- Convert("visium_brain.h5ad", dest = "h5seurat")
brain <- LoadH5Seurat("visium_brain.h5seurat")

# Spatial images are automatically reconstructed
Images(brain)
SpatialFeaturePlot(brain, features = "PTPRC")

2. AnndataR

github链接：https://github.com/scverse/anndataR
Installation

if (!requireNamespace("BiocManager", quietly = TRUE)) {
  install.packages("BiocManager")
}
BiocManager::install("anndataR")

pak::pak("scverse/anndataR", dependencies = TRUE)

Seurat to AnnData (h5ad)

# 一步到位：
write_h5ad(seurat_obj, path = "seurat_obj.h5ad")

# 分两步：
adata <- as_AnnData(seurat_obj)
adata$write_h5ad(path = "seurat_obj.h5ad")

AnnData to Seurat

# 一步到位：
seurat_obj <- read_h5ad(h5ad_file, as = "Seurat")

# 分两步：
adata <- read_h5ad(h5ad_file)
seurat_obj <- adata$as_Seurat()