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compbiomed / singleCellTK

Interactively analyze single cell genomic data
https://camplab.net/sctk/
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Prepare for upcoming Seurat v5 release #720

Closed Gesmira closed 4 months ago

Gesmira commented 9 months ago

I am opening this issue as a notification because singleCellTK is listed here as a package that relies (depends/imports/suggests) on Seurat. As you may know, we recently released Seurat v5 as a beta in March of this year, with new updates for spatial, multimodal, and massively scalable analysis. For more information on updates and improvements, check out our website https://satijalab.org/seurat/. We are now preparing to release Seurat v5 to CRAN, and plan to submit it on October 23rd. While we have tried our best to keep things backward-compatible, it is possible that updates to Seurat and SeuratObject might break your existing functionality or tests. We wanted to reach out before the new version is on CRAN, so that there's time to report issues/incompatibilities and prepare you for any changes in your code base that might be necessary.

We apologize for any disruption or inconvenience, but hope that the improvements to Seurat v5 will benefit your users going forward. To test the upcoming release, you can install Seurat from the seurat5 branch using the instructions available on this page: https://satijalab.org/seurat/articles/install.

Thank you! Seurat v5 team

joshua-d-campbell commented 4 months ago

singleCellTK v2.12.2 is compatible with both Seurat v4 and v5. The package can directly installed from GitHub:

library(devtools)
install_github("compbiomed/singleCellTK")

We will also push this version to Bioconductor soon.