Lukas Weber
Lukas Weber
Hi @lcolladotor , I'm not completely sure if this is the right place for this, but I found out there have been some changes to GitHub permissions / authentication affecting...
Hi, this is following on from our discussion in Bioconductor Slack (channel `#singlecell-queries`) from a few weeks ago. Thanks again for the update to propagate cellular barcode and UMI tags...
We previously included some functionality using `BumpyMatrix` to store molecule-based spatial transcriptomics data, along with an example dataset from the `seqFISH` platform in the `STexampleData` package. This is now obsolete,...
Currently it is possible to shuffle rows in `spatialCoords`, so that these rows become out of sync with the rows in `colData`. We could think about protecting against this in...
I was working with some SPE objects and noticed `cbind` has some unexpected behavior when subsetting spots from samples. Specifically, I have started with a SPE containing multiple samples and...
This was raised by @PeteHaitch on Slack. Currently when we create a SPE object containing multiple Visium samples with `read10xVisium()`, the column names (barcode IDs) are repeated, since 10x Genomics...
Hi, thanks for your previous responses a while back. I am now trying to use cellSNP/Vireo with a SAM/BAM output file from `salmon alevin` instead of Cell Ranger, and wanted...
See https://github.com/SamGG/diffcyt commits and email discussion
Currently in the [clustering](https://lmweber.org/BestPracticesST/chapters/clustering.html) chapter, we only have a short example using non-spatial clustering, and then list some alternatives for spatial clustering algorithms. @estellad We have had good experiences with...
Hi @estellad, thank you for getting in touch regarding adapting your workflow materials from the BC2 conference for inclusion in the book. As we discussed by email, I'm opening some...