-
Thanks to @pablo-gar for the bug report + suggestion.
>For slide-seq seems like a free-for-all based on whatever scale the contributors decide to use in obsm[X_spatial] , which defaults to having th…
-
Hi,
I'm interested in yout amazing work and try to take a through look on your data. But I found that nothing recorded in slideseq_beads_location.rds. All NAs. Would you check it?
-
The tool we use in for calculating optical/technical duplicate reads from the STARsolo BAMs requires a flag of 1024, which is captured in the BAM_FDUP attribute of the htslib.sam.h library used by Tag…
-
Hello,
How can I replace this step
```
...
bead
-
Hi Developers,
Thanks for putting up a great pipeline. I am trying to create alignment bam files (locally at hms outside broad) from the newly published [paper](https://www.nature.com/articles/s415…
-
Hello, it's a great work for spatial transcriptome analysis. I want to run your program on my custom dataset. How should I do? Thanks for your help.
-
Hello,
Thank you for making your code and data available! Would you mind also sharing the metadata for the P28 cells?
Thanks,
Salwan
-
Hello, When I run the T8_Batch.ipynb, I found a problem as following:
`
After flitering: (20139, 11750)
adata = adata[:, adata.var[highly_variable]]: (20139, 3000)
STAGATE_slideseqv2mob_batch…
-
Hi there,
Firstly - excellent tool! I really like the outputs so far.
I'm trying to map my single cell dataset onto my spatial dataset using RANK enrichment (script below from your website).
…
-
Currently it is possible to create Phrases that are going to be passed to the OpenCL backend that include C and OpenMP primitives such as `ReduceSeq`, while `OpenCLReduceSeq` should be used.
The di…