ktrns / scrnaseq

Workflow for single-cell RNA-seq analysis using Seurat
MIT License
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add export to h5ad for interactive visualisation with cellxgene #81

Closed fbnrst closed 3 years ago

fbnrst commented 3 years ago

Would be great to convert the final Seurat object to h5ad such that it can be visualized with cellxgene. This could just go next to the exports for Loupe and Cerebro. I would suggest to use sceasy for this (https://github.com/cellgeni/sceasy), this would add a dependency. Code would be something like:

sceasy::convertFormat(sc, from="seurat", to="anndata", assay=DefaultAssay(sc), outFile=paste0(param$path_out,"/anndata.h5ad"))