一行代码将h5ad转换为rds（其他常用格式也有）

一行代码将h5ad转换为rds（其他常用格式也有）

使用sceasy这个R包

安装：

devtools::install_github("cellgeni/sceasy")
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install(c("LoomExperiment", "SingleCellExperiment"))

转换：

sceasy::convertFormat('../data/citeseq.h5ad', from="anndata", to="seurat",
                       outFile='citeseq.rds')

下面是sceasy的github仓库

cellgeni/sceasy: A package to help convert different single-cell data formats to each other (github.com)

其他格式转换

Seurat to AnnData

sceasy::convertFormat(seurat_object, from="seurat", to="anndata",
                       outFile='filename.h5ad')

AnnData to Seurat

sceasy::convertFormat(h5ad_file, from="anndata", to="seurat",
                       outFile='filename.rds')

Seurat to SingleCellExperiment

sceasy::convertFormat(seurat_object, from="seurat", to="sce",
                       outFile='filename.rds')

SingleCellExperiment to AnnData

sceasy::convertFormat(sce_object, from="sce", to="anndata",
                       outFile='filename.h5ad')

SingleCellExperiment to Loom

sceasy::convertFormat(sce_object, from="sce", to="loom",
                       outFile='filename.loom')

Loom to AnnData

sceasy::convertFormat('filename.loom', from="loom", to="anndata",
                       outFile='filename.h5ad')

Loom to SingleCellExperiment

sceasy::convertFormat('filename.loom', from="loom", to="sce",
                       outFile='filename.rds')