单细胞之rds，loom和h5ad数据格式转换

Seurat依旧是单细胞分析的利器，也有越来越的的单细胞分析工具基于python开发。在数据分析时，有时需要将seurat的结果迁移到python下游分析，手动迁移seurat的cluster，umap，pca等结果很麻烦，现在和大家分享一款数据格式转换工具，帮助大家完成R与python多平台的多工具的数据分析。

工具来自这篇文章——Comparison of visualization tools for single-cell RNAseq data

安装与使用

这里是github上    README.md

Installation

sceasy is installable either as a bioconda package:

conda install -c bioconda r-sceasy

or as an R package:

devtools::install_github("cellgeni/sceasy")

which will require the biconductor packages BiocManager and LoomExperiment:

if (!requireNamespace("BiocManager", quietly = TRUE))

    install.packages("BiocManager")

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

To use sceasy ensure the anndata package is installed:

conda install anndata -c bioconda

Optionally, if you plan to convert between loom and anndata, please also ensure that the loompy package is installed:

conda install loompy  -c bioconda

You will also need to install reticulate package:

install.packages('reticulate')

Usage

Before converting your data please load the following libraries in your R session:

library(sceasy)

library(reticulate)

use_condaenv('EnvironmentName')

loompy <- reticulate::import('loompy')

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')