Trying to perform mapping between a refference dataset (seurat v3) and a query dataset (seurat v5) I am finding multiple issues. To try and debug the whole thing, I went back to trying to map two seurat v5 datasets, and I am encountering issues there too Using temp_reference as reference...
Also, in the beta version, the way one would save a bit-packing compressed and sketched SeuratObject was to use thesaveRDS()function in conjunction with the newly introduceddestdirparameter. This worked fine, but it was recently changed toSaveSeuratRds()without adestdirparameter (at least that...
Data quality-control The same quality-control workflows were applied to the 8-donor (Additional file 1: Fig. S5) and Zheng et al. (Additional file 1: Fig. S6) PBMC datasets using Seurat [32, 33]. First, cells with fewer than 250 RNA UMIs and genes with fewer than 3 UMIs across all...
In scRNA-seq analysis of the sorted data set, oocytes clustered with granulosa cells at a resolution of 0.1. In this case, oocytes were selected using CellSelector function in Seurat based on analysis of oocyte markers identified in the unsorted data set. Marker genes discriminating the ...
Hello, Thank you for your wonderful product! I am analyzing multiple datasets in parallel using a similar inferCNV code workflow. My datasets are integrated seurat objects which I have converted to inferCNV objects without issue. Four of...
In Seurat v5 we now include methods for mapping very large scale datasets to references via on-disk storage, as described here. This should address your issue I got the same error "Error in as.vector(x) : no method for coercing this S4 class to a vector" while I did MapQuery() out...
remotes::install_github("stuart-lab/signac", ref = "seurat5") Author elisulvaran commented Jun 27, 2023 Hello! Unfortunately, that didn't solve it either. However, I'm not sure if Signac was properly updated, because after running the line you provided, it looks like now I have versi...