# sceasy `sceasy` is a package that helps easy conversion of different single-cell data formats to each other. Converting to AnnData creates a file that can be directly used in [cellxgene](https://github.com/chanzuckerberg/cellxgene) which is an interactive explorer for single-cell transcriptomics datasets. | 💡 for h5da to rds conversion also see [https://github.com/cellgeni/schard](https://github.com/cellgeni/schard) | | ----------------------------------------------------------------------------------------------- | > ### Warning > Before installing the conda packages below please first create a new conda environment EnvironmentName and activate it. Everything else can be installed in R. ## 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') ```