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We are currently utilizing CellxGene VM (https://github.com/Novartis/cellxgene-gateway) to host a substantial spatial transcriptomic dataset comprising roughly 16 million cells. However, we are facing…
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Once markers are found that are differentially expressed between groups, it would be useful to show a histogram of this marker comparing the expression between the two groups, for each significant clu…
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https://github.com/r-bioinformatics/edgePy
Or something else for differential expression.
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From D4.1:
- [ ] Morisita Horn
- [ ] Bray-Curtis
- [ ] Jaccard
- [ ] Venn diagrams
- [ ] Cosine similarity
- [ ] Levenstein or Hamming distance to build network
- [ ] Bipartite graphs
- [ ] …
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Users have requested the addition of AOT and SOT lncRNAs to the GFF file in order to perform differential expression.
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Hi MNN group,
I see in the MNN help pages that it is not recommended to use MNN-corrected gene expression matrix for quantitative analysis such as differential gene expression. But I wonder if it i…
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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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In the workflow, sample 2 showed high expression of the up-regulated differential genes in qulescence, while low expression of the down-regulated genes in qulescence. So, sample 2 should have a high q…
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Goal: compare differential expression between a FNR knockout mutant and wild type _E coli_ MG1655 under anaerobic conditions.
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scVI used to have a within cluster DE test that I used often, but I no longer see this functionality in scvi-tools. Is it possible to add it back?
This would be a differential expression function w…