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.
๐ก for h5da to rds conversion also see https://github.com/cellgeni/schard |
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Before installing the conda packages below please first create a new conda environment EnvironmentName and activate it. Everything else can be installed in R.
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')
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')