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Collaborators have asked if we could implement a module for performing differential analysis.
After speaking with Dan T., we believe that we can do so in the existing application without bogging t…
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Hello, after running saw reanalyze diffExp, I only saw 3000 genes in the output file *.find_marker_genes.csv. Is there a way to make it output all genes even if no differential expression is found? Th…
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Hello,
I'm working with a single cell dataset, which has imperfect cell isolation, and has some mis-labeling of counts between cells. We can estimate the level of "contamination" for each cell, for…
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### Is your feature request related to a problem?
Is there a way to do differential expression of transcripts (e.g. similar to DEseq2 but for transcripts) with RNAlysis?
### Describe the solution yo…
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I’m facing an issue with the report below.
we have a total of six samples divided into two groups: treated and control. Each sample has been processed independently up to the DE Analysis step, w…
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# Grading Assessment for Daniel Mendoza-Sanchez
## R Script Components
### 1. Data Loading and DESeq2 Object (1 point)
Score: 1/1
### 2. VST and PCA Implementation (1 point)
Score: 1/1
#…
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I am using diffxpy to calculate differential gene expression analysis, but every time the iteration for the calculation starts and is ended quickly with the same error. What could be the reason?
Th…
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### Description of feature
Blocked by https://github.com/owkin/PyDESeq2/issues/213
See also https://github.com/theislab/pertpy/blob/2cc7ff77695cb616bb3ab207b5e506c0880aadb1/pertpy/tools/_different…
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I've been using Harmony for batch effect integration, but I would like to be able to continue downstream analysis in Seurat using the corrected data. I read [this review](https://genomebiology.biomedc…
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### Ask away!
Hi,
In main.nf, input_reads is fed to differential_expression() and in differential_expression.nf the workflow differential_expression {} has full_len_reads defined. I've seen workfl…