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- green = wt accessibility
- orange = mt accessibility
- blue= max( 0 , wt - mt ) : accessibility increased
- red = max( 0 , mt -wt ) : accessibility decreased
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Could be downstream of https://github.com/tidyomics/genomics-todos/issues/1
Work through multi-sample multi-condition differential test using pseudobulked counts, a la a hybrid of `muscat` and `csaw`
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Hi,
For the differential accessibility function, `diff_acc
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Testing for differential expression/accessibility is embarrassingly parallel, and could use all available cores by default.
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## Hierarchy of RE
```
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup1 (Transcript)
LTR (Family) —> L1 (Sub-Family) —> L1_Rod (Gene) —> L1_Rod_dup2 (Transcript)
LTR (Family) —> L1 …
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- [ ] ATAC
- Work in progress: https://github.com/openpipelines-bio/openpipeline/issues/398
- [ ] CCC analysis
- Robrecht lift over from Open Problems?
- [ ] DE analysis
- [ ] Gene signatures…
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**User story**
For clusters / cell types / cell sets which have been defined upstream, differential expression / accessibility can be computed for each cell set by comparing to all (or all other) c…
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Hello,
It seems that the function to plot the GRN on python doesn't work anymore since the recent updates:
from scenicplus.networks import create_nx_tables, create_nx_graph, plot_networkx, expor…
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when performing differential peak analysis (function findDAR), ie comparing accessibility across clusters, is there any normalization done during the process? I understand it is using exact test?thank…
ghost updated
5 years ago
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### Current Behavior
This is sometimes described as “too deep”, “too advanced” (I view this adjective as a negative thing re: accessibility). Taking a page from psychotherapy canon / law enforcement …