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Hi, While reading the data processing code you gave me, I noticed that you used some preprocessed files,
such as data.feather,
anno.feather,
good_fenes_beta_score.csv,
…
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### Project short name:
InflammatorySkinPathologies
### Primary Wrangler:
Ida
### Secondary Wrangler:
### Associated files
* Google Drive: tbd
### Published study links
* Paper: [Second-Strand S…
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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…
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Hello, thank you for this tool! It would be very useful for me as I have scRNA-seq, scATAC-seq and proteomic data.
I would like to incorporate the PPI data into the GRN.
I saw this information in…
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When I did cNMF in spatial transcriptomics, in which the n_counts of one spot could be smaller than scRNA-seq cell. It usually encounter that I have to drop many spots, due to there is no highly varai…
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Hi, Alex
Apologies if I have missed this somewhere, and I am trying to process my 10X data with STARsolo. This is very convenient. But if there were more than one barcode and UMI molecular in my s…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`): 1.2.9
- OS name and version (`lsb_release -ds`):
**To Reproduce**
Exact bcbio command you have used:
```
bcbio_nextgen.py /user…
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Single-cell RNA-seq with spike-in cells enables accurate quantification of cell-specific drug effects in pancreatic islets
https://doi.org/10.1186/s13059-020-02006-2
Data: https://www.ncbi.nlm.nih.…
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## R4.1.0 on T460P
the functions are outdated.
![image](https://user-images.git…
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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…