-
When I do the step 9.3.3 I receive this error:
> concat_spe
-
Hello!
I want to use this sample (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM7473682) to generate Seurat object for clustering and subsequent cell-cell interactions inference. This sampl…
-
First reported by @Erik-D-Nelson at https://jhu-genomics.slack.com/archives/C03KD30V3ST/p1657043593610579
> I was using R version 4.2.0, `SpatialExperiment` version 1.6.0, and `spatialLIBD` versio…
-
If `colPairs()` contains a `SelfHits` object with no metadata columns then `colPairs(x, asSparse = TRUE)` fails with a cryptic error. Example based on the documentation:
```r
library(SingleCellExp…
-
Hi there - apologies in advance if this is very obvious - my collaborators processed our data using `Seurat` and noticed a discrepancy between their `Count_RNA`/`nFeature_RNA` and by `sum`/`detected` …
-
Hi, Nick,
I was able to run the codes finally as below, but two Warnings came up. Note, it only came up with `normalize=T`.
I wonder how I might check to assess whether this Warning influenced …
-
Hi,
I am getting an following error when I tried to plot the UMAP using DimPlot function from seurat v5. I have used several analysis with seurat and used the same function many times with the previ…
-
Hi,
I am very pleased that SPATA2 has helped me so much in analyzing signal trajectory, and the plot produced by the function is pretty nice.
However, I was interested to know if there was a way to …
-
hello,
I have been trying to use Banksy on Xenium data and I have also tried to embed the coordinates inside the object but I still can't runBanksy function on ir because it lacks computebanksy matr…
-
Hey! Thanks for an easy-to use package - was a breeze to get running. Quick Q: is there any native support for multiple samples? E.g., say by SPE contains many replicates (more than one `sample_id` in…