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- [ ] ATAC
- Work in progress: https://github.com/openpipelines-bio/openpipeline/issues/398
- [ ] CCC analysis
- Robrecht lift over from Open Problems?
- [ ] DE analysis
- [ ] Gene signatures…
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gene expression datasets (LDS-1481, LDS-1484)
http://lincsportal.ccs.miami.edu/signatures/datasets/LDS-1481 returns and http://lincsportal.ccs.miami.edu/signatures/datasets/LDS-1484 does not retur…
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Following error when I try to run the PBMC-scRNA notebook:
```
/clustergrammer_fun/categories.py in dict_cat(net, define_cat_colors)
131 for inst_full_name in inst_dict:
132 …
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Dear Dvir,
I am currently working with bulk gene expression data obtained from microarrays. My specific aim is to infer gene expression specific to epithelial cancer cells by regressing out signals…
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Hello! I am trying to use SCINA with a very big dataset, it is ~ 25.000 genes and 80.000 cells. I Have a very large file of signatures downloaded from CellMarker (1600 signatures), but I filtered out …
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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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Hello,
When I plot radars I can see gene expressions but when I try to plot signatures, I don't see them. Why could it be?
`
plot.states.radar(ref, query = query.projected, genes4radar = progra…
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UK Biobank Pharma Proteomics Project (UKB-PPP) is described in this paper https://www.nature.com/articles/s41586-023-06592-6 . Among the analyses presented there is an association analysis between pr…
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Hi.
I met an error and there is nowhere to debug. Can you please give some hints?
```
scaled_counts
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Hello, I'm using SCINA_1.2.0 with R version 4.3.2 (2023-10-31).
When I plotted the heatmap on my dataset, I noticed that the legend for the column colors listed all signatures as opposed to those act…