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Provided that the user has supplied an expression /rank file often there are genes that are highly differential but are not covered by any of the genesets that are present in the enrichment map. It w…
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My goal of this exercise is to be more familiar with Differential gene expression with RNA-seq.
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# MA plot
[Wiki page](https://en.wikipedia.org/wiki/MA_plot)
[Interpretation of differential gene expression results of RNA-seq data: review and integration](https://dx.doi.org/10.1093%2Fbib%2Fbby…
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@skchronicles said
> @kopardev
> Yes, I will look into it.
>
> I was also thinking we should create a custom set of references for the ci workflow.
>
> Here is what I am thinking:
>
>…
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Hello,
I really enjoyed your paper (great method!), and I am applying spaCET for deconvolution of a lung cancer ST Visium data set. For validation, I would like to know how to find the marker genes …
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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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Add documentation explaining features that don't work in either of the three object formats. For example, SingleCellExperiment objects don't support subsetting based on feature expression, or differen…
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Hi! In terms of differential expression, what genes from the three categories (DEa, DEg, DEs) are worth considering for further analyses? Thanks!
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- [ ] Heatmaps
- [ ] toggle function for y-xaxis clustering
- [ ] cluster selection
- [ ] Inter-cluster differential expression testing
- [ ] Annotation functionality
- [ ] annotate w…
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671649/
Background
The schistosome esophagus is divided into anterior and posterior compartments, each surrounded by a dense cluster of gland cell…