Seurat to SCE error "Error: Unsupported conversion from "seurat" to "sce"

cellgeni / sceasy

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

GNU General Public License v3.0

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Seurat to SCE error "Error: Unsupported conversion from "seurat" to "sce" #16

Closed levinhein closed 3 years ago

levinhein commented 3 years ago

Hi. Do you have any idea why this doesn't work?

> library(sceasy)
Loading required package: reticulate
> library(reticulate)
> use_condaenv(condaenv = "scgen-env", required = TRUE)
> loompy <- reticulate::import('loompy')
> #Seurat to SingleCellExperiment
> sceasy::convertFormat(TC.combinedFINAL, from="seurat", to="sce",
+                       outFile='TC.combinedFINALsce.rds')
Error: Unsupported conversion from "seurat" to "sce"

nh3 commented 3 years ago

This function requires R package Seurat (it basically calls the function Seurat::as.SingleCellExperiment()). Have you checked if it's installed in the same environment as sceasy?