seb-mueller/sceasy

A package to help convert different single-cell data formats to each other

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 which is an interactive explorer for single-cell transcriptomics datasets.

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 (with scipy==1.2.1) is installed:

conda install anndata==0.6.19 scipy==1.2.1 -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')