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theislab / scib

Benchmarking analysis of data integration tools
MIT License
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scIB-R-integration environment has R version 3.6.1 but Seurat depends on R version >=4.0 #239

Closed rogershijin closed 3 years ago

rogershijin commented 3 years ago

I get the error package ‘Seurat’ is not available (for R version 3.6.1) when trying to install, is there a way to get around this? Thanks!

LuckyMD commented 3 years ago

Hi @rogershijin,

I’m pretty sure there is a version of Seurat that is compatible with R 3.6.1. We were using Seurat 3.1.1 and 3.0.2 in the benchmark i believe. Could you install an older version of Seurat in the environment? Otherwise, we are just working on an updated environment for further use of the pipeline in the scib-pipeline repo in a PR as well. More installation instructions are there as well. Maybe check that out to see if that helps?

rogershijin commented 3 years ago

Thanks @LuckyMD! Was able to install Seurat 3.2.0 by installing old versions of rsvd (0.9) and spatstat (1.64-1).