Thanks for the tools. I was able to convert my Seurat obj (19890 cells x 16003 genes) fully processed via SCTransform workflow to h5ad file. However, when I examined the number of genes in Python, it shows 19890 cells x 12432 genes. Would you mind letting me know how to resolve this ...
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 ...
dbdimitrovmentioned this issueJul 27, 2022 pakiesslingmentioned this issueNov 21, 2024 SingleCellExperiment/Seuratshould containdgCMatrixinstead ofdgRMatrixscverse/anndataR#202 Closed Sign up for freeto join this conversation on GitHub. Already have an account?Sign in to comment...
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(sc...