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https://academic.oup.com/bioinformatics/article/36/9/2657/5701648
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Hello,
After reading your paper, I became very interested in Omicverse. After learning more about it, I found that Omicverse provides great convenience for data analysis. However, I encountered some …
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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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Hello,
I have recently started using STAGES with RNA-seq data. I did the statistical analysis previously with Rstudio and generated three csv files with p-values and ratios of three different compari…
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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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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…
melop updated
2 weeks ago
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Hi,
I am a newer in small RNA analysis and I have run the analysis with the pipeline successfully according to your instruction.
But considering the output, I have a doubt about the differentia…
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## Bug report
### Expected behavior and actual behavior
I would anticipate that passing arguments such as `--minimap2_args '-k15'` would result in the parameter `minimap2_args` being set to t…
cjw85 updated
1 month ago
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I am using the FragPipe software for database searches, and the output file combined_ion.tsv is used for quantification with directLFQ. I plan to perform differential expression analysis using DEqMS, …
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Right now, validate-differential expression is made up of two notebooks. One that sets up a practice dataset to compare to, and the second that does the actual comparison. We have to think about how t…