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=...
AnnData ↭ SingleCellExperiment RPy2 converter fromAnnDatatoSingleCellExperimentand back. (Fordetails about conversionsee thedocs) You can for example use it to process your data using bothScanpyandSeurat, as described in thisexample notebook ...
Raw sequencing reads were processed with Cell Ranger 5.0.0 to generate the gene count matrix. Seurat R package 4.0.1 was used for downstream expression analysis. Due to variance in the sample’s sequencing depth, different cell filters were applied. Sample 1 and 2: gene number > 3000,...
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') ...