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We will initially proceed with our initial decision to split 'Predicted' from 'Experimental' Functional impact annotations - and model these as separate VA types. Our rationale was that:
- they have …
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Hi infercnv team,
I am running infercnv with the following command:
```
infercnv_obj = infercnv::run(infercnv_obj,
cutoff=0.1, # cutoff=1 works well for Smart-seq2, …
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#### Current behavior:
24 genes are discovered to be uncorrelated with their corresponding reactions in Vitamin A/B2/C/D/E metabolism.
| Gene| UniProtID| Reaction| GPR| Correlation| Manually…
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Hi there
Maybe a basic question but I'd like to ask what people's opinion is of using DESeq2 within SQMtools for differential abundance of taxa? It's obviously possibly with SQMtools to compare dif…
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Which columns should be made accessible in the var dataframe in census?
Right now, census only has a subset of the columns specified in the cellxgene schema. In census, there are:
* `feature_id`…
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New CHM13 genome provides only `*.gff3.gz` files for genes annotations, see https://github.com/marbl/CHM13#v11. So we cannot configure genes markup for new genome in JBR
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## Issue
Tabix throw error that omim bed file generated from howard is not sorted (likely gene on negative strand are not correctly inserted in the bed file)
### Omim bed annotation creation
ho…
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**Describe the bug**
Hello, I'm trying to run SCENIC+ using SnakeMake in a linux machine (centos 9), on the tutorial dataset.
I ran scATAC-seq preprocessing in python (using pycistopic, using the tu…
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#### Current behavior:
24 genes are discovered to be uncorrelated with their corresponding reactions in `Xenobiotics metabolism`.
| Gene| UniProtID | Reaction| GPR| Correlation| Manually…
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When I was running copyKAT from seurat object, the code is:
subset_count