seurat-object
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satijalab
Change `pbmc_small` from a binary Rda file to an R script. This change - provides a record of how `pbmc_small` is generated - provides the raw MTX for `pbmc_small` -...
Hello, maybe this is expected behavior, but I was surprised when I updating an object `v3.99` to `v5.0.1` that the new object still contained the old data structure: slots instead...
I and others have posted about issues related to V5 assays that have a single cell. While an assay with one cell is probably a fringe case and usually not...
This is meant to help diagnose issues when assay doesn't have desired layer. For example see satijalab/seurat#8658 and discussion in satijalab/seurat#8659, specifically the [suggestion from Sam](https://github.com/satijalab/seurat/pull/8659#issuecomment-2009820323). The warning message might...
Added notes in documentation for add.cell.ids parameter in merge.Seurat to specify that id's are added as prefixes for RNA data but added as suffixes for ADT data.
Hello, I have a suggestion to add an NA-excluding function such as `which()` in line 18 of the function _CellsByIdentities_, to produce more sensible output for the edge case when...
For purposes of anonymization I need to rename the cell-names which include the study number in our dataset. I have a Seurat-object with `test@assays$RNA$counts@Dimnames[2])` and `test@assays$SCT$counts@Dimnames[2])` having for instance: `"aab1.P2.299"...
Hello, first thank you for developing such great tools I am Ruba PhD student in Germany and I am doing scRNAseq analysis for my data, I wanted to check the...
Hi, I have been running Seurat for data analysis on version 4.3.0.1 along with SeuratObject package 4.1.3. Until a few weeks back, all the analysis was running fine but from...
`SpatiallyVariableFeatures()` throws the following warning with R4.1 and Seurat 4.0.4: `Warning in xtfrm.data.frame(x) : cannot xtfrm data frames` I think this crops up in line 501 of `assay.R` when `order()`...
