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Dear Simone,
Congratulations for the tool, it is great being able to call allele-specific copy number in single cells and get the most of the data. At our lab, we have generated standard single-cell…
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This check should be performed by the pipeline upstream (ping @hassanfa), but Scout could show the result of the check.
From the notes of the last user meeting (#1679)
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I created a new gene panel, and added to the institute: "trusight1". Now I want to show it in the filters of all those cases for that institute. It only shows HPO and The Panel, but not Trusight. Shou…
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FastQ files for case Toughdingo are corrupted OR they are unsorted. It seems like concatenation step in `cg` is misbehaving probably due to sequence top up.
This case has been previously analyzed t…
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## Issue
There are two issues. First, feature barcode syntax. Second, combining VDJ workflow with new scRNAExpression-CellRangerFastq workflow.
### Feature Barcode
Currently, FONDA uses 'old' cel…
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**Submitting author:** @lincoln-harris (Lincoln Harris)
**Repository:** https://github.com/czbiohub/cerebra
**Version:** v1.2.0
**Editor:** @lpantano
**Reviewer:** @betteridiot, @afrubin
**Archive:** …
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Dear Developers,
Recently, I have been reading your scTensor pre-print paper which looks interesting and I would like to have your opinion regarding using it for complex tumor microenvironment proj…
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Comparison of genomic/transcriptomic features and derivates such as TMB, pathway activity, etc... to survival. Determine markers that could add prognostic values to different PBTA cancer types. KM Plo…
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**Background**:
Genetic sequencing has confirmed that many cancers are evolutionarily heterogeneous. As a tumor grows, new mutations accumulate in individual cells, and as these cells replicate, the…
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I get this error that I don't understand fully
```
> infercnv_obj_default = infercnv::run(
+ infercnv_obj,
+ cutoff=0.1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x…