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I'd like to limit the expected_cell_types parameter in deconvolute_xcell(). It would be very helpful if it were easy to get a list of these cell types within immunedeconv.
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For some reason, a very large portion of the values in the `p`, `padj`, and `lfc` arrays are NAs and I'm not sure why. I am using the raw counts for the bulk RNA-seq as input to CAR-seq.
Any help …
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Creating this issue to keep track of random ideas for project name
@maximz :
> something simple like "infiltrate" or "infiltration" could work, or maybe a quasi-synonym like "percolate"
Some…
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> Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumor-infiltra…
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Some questions
* Will FACS sorting disturb RNA?
* How should we preserve the cells post-sorting and pre-RNA isolation?
* How should we isolate RNA?
* What markers should we sort on?
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https://mp.weixin.qq.com/s/TnUq-NfIc7oQTjnflVqs4g
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I have a makeflow file with ~17K commands. Some of them at the root of the tree
```
dev/test_simulation/input__slope_0.5__foreignProp_0.8__S_30__whichChanging_1__run_2.rds:
Rscript ~/PhD/…
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@andrewelamb, adding the argument `cohort` to a query makes it return no results. Example below:
Before:
```
#getting ICI data
#datasets that we have in the iAtlas database
ici_datasets
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I somehow can't get to work cibersortx locally when using one of the following options
* `--absolute TRUE`
* `--rmbatchSmode TRUE`.
In both cases, the resulting cell-type matrix contains onl…
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### Your suggestion
It is requested all too regularly on RT. Document how to do this, including a video :+1: