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When I used "AUCell" and "VISION" method in sc.metabolism.Seurat, I got different errors.
`scRNA_metab
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Dear,
Is it possible to use EPIC for cell type deconvolution using ATAC-seq datasets?
It gives the following error when I provide bulk ATAC-seq matrix (rows=peaks, columns=sample/subject) as inp…
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- [ ] a. Correlation of RAS pathway signature gene expression with mesenchymal exposure values of primary tumors.
- [ ] b. Correlation of JUN/FOS target gene expression mesenchymal exposure values of…
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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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hi,
A bug occurred when I was using scanpy for high variant gene arithmetic. I learned that the bug originated from scikit-misc, so I came to you for help.
>my code:
`adata.layers["counts"] = a…
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Hi!
First off, thank you for this analysis tool!
I am analyzing some Perturb-Seq data and have followed the vignette. I ran Mixscale_Scatterplot and interestingly the perturbation score seems p…
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**User story**
Input a gene list (i.e., the user selects multiple genes)
**Preferred solution**
Render a visualization using a linear combination of the expression values for the selected ge…
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Hi,
Ly6g is a good mouse neutrophil marker (therefore probably will be included in the gmt file neutrophil signature).
I noticed that this gene is missing in besca/datasets/homologs/MGItoHGNC.csv…
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Millions of transcriptomics samples were generated by the Library of Integrated Network-Based Cellular Signatures [(LINCS) program](https://lincsproject.org/). When these data are processed into searc…
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It would be useful to be able to specify custom signature matrices.
Originally proposed by Sonja Hänzelmann via email and also mentioned as one of the "masked options" by @jracle85 in #14.
Pro…