-
Dear Dr. Satija
"If uploading a Seurat object, it must contain an assay named ‘RNA’ with raw data in the ‘counts’ slot. Note that Azimuth uses only the (unnormalized) counts matrix."
Could you p…
-
Hi, I am starting with CITE_seq-Count and its output. The Tool looks amazing.
After running the script I got an output that is very populated by unmapped TAGs. I can recover few cells mapped to my …
-
Hi,
Thank you for your great tools for single cell multi-omics analysis. I successfully ran the cite-seq demo but failed to ran our scRNA+scATAC data with following error report:
The input …
-
- [ ] Antigen affinity score
* Incorporates AVID-seq counts and total receptor counts (CITE-seq/GEX counts)
- [x] Add VDJ data from cellranger to Seurat object
- [x] Receptor diversity
* inver…
-
Does sfaira already deal with multimodal data in some way, such as
* RNA-velocity
* VDJ information
* CITE-seq?
-
### Description of feature
This issue is to provide an overview of different tools and related sub-issues related to supporting multiple modalities:
- CITE-seq (=RNA+protein) (https://github.co…
grst updated
6 months ago
-
So I had a question about running on multiplexed chemistries. Things like 10x flex, as well as CITE seq. At least with 10x flex, you have a pool of probes that can barcode a few samples. It comes in 1…
-
I have a complex whitelist, as my scRNA-seq pooled samples were generated using the BD Rhapsody system. Essentially it has a CB region from 0-8, 21-29, 43-51 and UMI position 52-59. The antibody barco…
-
Hello Team,
Thank you for the wonderful tool. However, I have two questions:
When I run `RAT,` it gives an error related to the reads with the following message. From what I understand, my `FAST…
-
Everything looked to be running fine:
```
!CITE-seq-Count \
-R1 $Hash_R1 \
-R2 $Hash_R2 \
-t feature_barcode_onlist.csv \
-cbf 1 -cbl 16 \
-umif 17 -umil 28 \
-wl 737K-august-2016.txt \
-T 8 …