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Hi
I've question, whenever xCell performs the ssGSEA analysis, it only uses the ~10,000 genes from the immune signatures, right? So, no problem if the input matrix is a 60,000 transcript or just 20…
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### Description of feature
* [DoRothEA](https://saezlab.github.io/dorothea/) provides curated transciption factor activation signatures
* [PROGENy](https://www.bioconductor.org/packages/release/bi…
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Hello,
I just finished reading your very interesting paper. I was wondering if you also had a lot of non-synonymous mutations to the genes ebh, sdrC, sraP. If so, why did these genes not show any a…
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hello,
**Describe the bug**
My shell:
```
pyscenic aucell \
scenic.loom \
reg.csv \
--output pyscenic_output.loom \
--num_workers 5
```
My log
```
2024-06-13 13:14:58,9…
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I propose to develop a new function that uses a combination of `simplify` and `getGOLevel` to reduce the redundancy of GO terms. *The main idea is that if two terms have a high similarity, the more ge…
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### Add the NIH LINCS Program landmark genes to gene_lists
The list of 978 landmark genes is here:
https://clue.io/command?q=/gene-space%20lm
The NIH Library of Integrated Network-Based Cell…
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Hi,
I am using a little selection of immunegenes from a panel of oncogenes from HTG experiment
and I have totally 1402 genes.
Can I run XCell following any instructions? My error is;
scores = ra…
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Hi,
I realized that some of the genes that are not shared for both spliced and unspliced info are filtered in the beginning of the velocyto pipeline. During the velocity I would like to show some o…
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Using the app itself as an interface should be self-explanatory. What is not self-explanatory is what the biological meaning behind all of the app's functionality is. @ajlee21 Suggested a while ago th…