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- [x] a. Consensus SE Tumor's signal NMF H matrix
- [x] b. Consensus SE Cell line's signal NMF H matrix
- [x] c. Consensus SE Tumor and Cell line's signal UMAP
- [x] d. NMF riverplots
- [x] e. Co…
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Hi nakul:
Recently, I used the TEprof2 to find some interesting TE-gene chimeric transcripts. But I suspect it may happen in noramal tissue. The STEP12 write "In the case of our publication, we fil…
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I think it's likely that there is a general expression pattern for how mutated a tumor is. For example, super mutated tumors may have wacky gene expression, solely because they're super mutated and no…
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Basic idea is to create generative model with such structure that would allow to disentangle features in our datasets.
Particularly disentangle variability in gene expressions coming from tumor type …
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Hello
What is meant by Normal Expression data? In cancer research we RNAseq tumor only usually
Thanks
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### Project short name:
MetastaticLUADReprogramming
### Primary Wrangler:
Ida
### Secondary Wrangler:
### Associated files
* Google Drive: [folder](https://drive.google.com/drive/folders/19DQaa_vy…
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- will map terms from [oba-efo-unreviewed.dosdp.tsv](https://github.com/obophenotype/bio-attribute-ontology/blob/master/src/mappings/oba-efo-unreviewed.dosdp.tsv)
- filtered by **attribute_label**: _…
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Source: GEO
```yaml
label: GSE79021
title: >
Gene expression profiling of human prostate tumors identifies chromatin
remodeling as a molecular link between obesity and lethal prostate can…
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Hello,
I have been using Numbat for quite sometime now, and it has worked great. Recently we switched to the 5' 10X protocol. Numbat fails to correctly identify the CNVs, and in all samples i keep …
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https://github.com/federicomarini/quantiseqr/blob/94e91fc190c8d876b15c0ae52199a5e7deb0f9ab/R/quantiseqr_helpers.R#L433
I am attempting to run quantiseq on the expression data from TCGA-STAD which I…