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As a scanpy user who has already computed differential expression via `scanpy.tl.rank_genes_groups` and saved the results to `.uns['rank_genes_groups'`], I want to view these results in cellxgene so t…
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Hello JSB-UCLA,
I have a question for you. I was looking for synthetic scRNA seq data that would resemble my own scRNA seq data sets and which I could use to test the performance of two methods of …
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Hi,
The program successfully predicts the fusion gene in the ceil line but I would like to do some downstream analysis to compare the expression for this fusion gene between samples.
Are those ju…
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Hello @brianjohnhaas
I'm doing DEG recently. Refer to the reference steps, I found that there seems to be some problems with the R installation application package in linux (as shown below).
![I…
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Blurb / summarize this: https://www.biorxiv.org/content/10.1101/2024.08.02.606405v1.full.pdf
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- [x] Gene set enrichment with `fgsea`.
- [ ] Phenotype prediction (with `phenopredict`?).
- [x] Differential expression with limma and proper design matrix.
- [x] Differential expression with DESe…
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Dear Team,
We noticed a strange behavior of the DESeq2 module when used inside the NFcore differentialabundance pipeline. DESeq2 allows to testing for differential expression with null hypothesis logF…
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```
from sympy import *
a, b, k, m, n = symbols('a b k m n', cls=Wild)
x = Symbol('x')
pattern = x**n * (a + b * x**k)**m
expr = x**(S(1)/3)*(3 - x**2)**(S(1)/3)
expr.match(pattern)
```
It w…
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Correct defintion
FROM:
A differential expression analysis data transformation is a data transformation that has objective differential expression analysis and that consists of
TO:
A diff…
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Hi,
I am attempting to load stringtie output data into R but get multiple errors in doing so:
data_directory = system.file('extdata2', package='ballgown')
bg = ballgown(dataDir=data_directory, sampl…