7.2 Clustering using scran

Additionally, ArchR allows for the identification of clusters with scran by changing the method parameter in addClusters().

projHeme2 <- addClusters(
    input = projHeme2,
    reducedDims = "IterativeLSI",
    method = "scran",
    name = "ScranClusters",
    k = 15
)
## ArchR logging to : ArchRLogs/ArchR-addClusters-973a2c43-Date-2025-02-06_Time-01-01-47.534412.log
## If there is an issue, please report to github with logFile!
## 2025-02-06 01:01:49.387429 : Running Scran SNN Graph (Lun et al. F1000Res. 2016), 0.022 mins elapsed.
## 2025-02-06 01:01:50.742487 : Identifying Clusters (Lun et al. F1000Res. 2016), 0.045 mins elapsed.
## 2025-02-06 01:06:24.969245 : Testing Outlier Clusters, 4.615 mins elapsed.
## 2025-02-06 01:06:24.975199 : Assigning Cluster Names to 9 Clusters, 4.616 mins elapsed.
## 2025-02-06 01:06:25.046268 : Finished addClusters, 4.617 mins elapsed.