-
Hi! Excited to try out this tool.
I currently have cell barcodes with corresponding cell-type annotations but the cells/barcodes that were filtered out when I processed my data in Seurat are still …
-
Hi Milo lab,
Thanks very much for providing such a user-friendly tool for annotating spatial transcriptomics.
I've been attempting to isolate/subset specific cell types within a region of inte…
-
Hi,
We have 10x data from a cell village and I am trying to identify donors in the village using donor assignment. I have the 10x bam file, barcodes.tsv, gtf and vcf files.
Step 1: I ran Drop-seq…
-
Hi Yuntian,
Thank you for developing this excellent tool! We are currently exploring the possibility of combining the LongcellPre pipeline with SCOTCH (https://github.com/WGLab/SCOTCH?tab=readme-ov…
-
Hello -
In some workflows that could use umi-tools, we already have an explicit whitelist of the corrected cell barcodes. There is still a need to identify the non-error-corrected cell barcodes.
…
-
Hi， @M0hammadL， @b-schubert， @ArcaneEmergence， @irene-bonapa and @drEast
I am currently working to reproduce your meaningful study, "Multi-modal generative modeling for joint analysis of single-c…
-
Hello
I have a question/issue regarding the polyA requirement. So far, I have been using BAM files that were aligned using the ISOSEQ pipeline. As part of this pipeline, polyA tails are trimmed (`…
-
**Describe the bug**
Hi there,
I‘m using ArchR to analysis my ATAC data. And I want to do barcode filtering in `createArrowFiles` step. I found that `getValidBarcodes` could help me extract the val…
-
Hi,
I am running copykat on my single cell data from mouse. It runs with no problems in all the samples except this one, which should be all tumor cells and I can´t understand why. My tumor cells h…
-
### Is your feature request related to a problem? Please describe.
I want to have capability to use different fonts within a table, for example I need to create a table, where some fields are just …