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By Oct 25:
- [x] add units/measure to configuration and visualizations
Heatmap
- [x] add annotation columns/rows for heatmap (curated list)
- [ ] toggle heatmap orientation? columns=omics vs colum…
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Hi
I am using monocle for differential gene expression analysis of single cells. I am trying to compare the expression of genes of a cell subpopulation (a cluster in tSNE plot for example) for two di…
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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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While running sc.metabolism.Seurat function, I encountered an error in "Computing differential signature tests..." step.
It mentioned that Error in `[dense coercion: allocating vector of size 3.1 Gi…
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After clustering cells with a restricted gene set, I would like to see the contribution of "specified genes" in subgrouping the cells.
`sc.tl.rank_genes_groups` uses all the genes in the background …
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How can we elucidate the ground truth for the mol_mrna from the dyngen object?
I am following the tutorial [here](
https://dyngen.dynverse.org/articles/getting_started.html#step-5-simulate-gold-st…
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After running `TreeTerminus` on the samples in my RNA-seq experiment and obtaining the consensus tree, I am using beaveR to parse that output. I was hoping to clarify some details about the output of …
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Currently we only support testing a specific contrast (either via a coefficient or a contrast vector), but we often do differential expression analysis where we want to test mean shifts in several gro…
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I am not looking to do differential expression so I did not open the DE module.
However, I would still like to normalize the count data with transcript length.
Is there any way to obtain this f…
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Hi,
thank you for providing such a fantastic tool! It’s exactly what I needed for integrating GWAS summary data with scRNA-seq data.
While using this tool, I encountered a question regarding th…