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Need new term oogonia or whatever the zebrafish equivalent is in ovaries
stage adult-adult
need to have stage 1a and stage 1b as is_a children of stage 1 oocyte to be able to curate differential gene…
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Related to #9, here is an outline for a proposal for an interface based around a single function (I call it `qtn` below for "quantized tensor network" but open to suggestions) which at a high level ac…
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# Data overlap
## Generate a `data overlap matrix`. Overlapping to the `ATAC-Seq differential accessible regions`
- [x] **ChIP-Seq:** `TRUE` or `FALSE` of there is an overlap between ATAC-Seq an…
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Hello
I want to use sRNA bench to preprocess my data but I would like to perform differential expression in other platform. I couldn't find any kind of count table in the bulk results. Am I missing a…
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Hi,
Thank you very much for this very useful package!
As written in your vignette : " If batch effects are present in the data, these should be accounted for, e.g., using Seurat or Harmony, to…
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Hi, thank you for providing such a great tools.
I am currently analzying UTR length shift using the function "DetectUTRLengthShift". Among the parameters of DetectUTRLengthShift function, you can …
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First of all thank you for this nice tool.
I run nebula for differential expression analysis between 2 groups and I realised that my top (by logFC) significant genes are mostly driven by some outlie…
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I always get an error when I use scripts to process data with differential expressions
CMD: R --vanilla -q < genes1.counts.matrix.F2n_vs_M2n.DESeq2.Rscript
sh: R: command not found
Error, cmd: R --…
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Hi,
In the readme, you suggest that the delta variance for a DE gene should be checked, and that DE genes that also have "high" variance are likely false positives. It would be great if the calcula…
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Feature request
I've been trying to plot a subset of a ranked list (gene differential expression dataset). I would like the minimum and maximum color scale set to that of the original complete rank…