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Hello,
I am performing a GWAS (mixed effects) and correcting for population structure using a phylogenetic tree and your script --
python tools/pyseer/scripts/phylogeny_distance.py --lmm tree > si…
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Hi @lea1010 @niekverw
Thanks for your beautiful code !
I meet a problem when I use ukbpheno example data to learn how to use ukbpheno.
I want to generate binary phenotype about HfInCad.
`…
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Dear author
I have produced a vcf file from the Panaroo output core_genes_alignment.aln and selected a few SNPs of interest using a GWAS approach. My question is: how to find in which genes are tho…
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## 1. Bug description
I tried running MSS use the latest version (1.5.12) and got errors. Any help would be appreciated!
### Console output
```
Formatted summary statistics will be saved to…
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## 1. Bug description
Assigning wrong N to metadata.
I think this is some error with now I'm inferring N from "ncase" and "ncontrol" when the "sample_size" column is NA.
Specifically, I must be …
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### Affected tool(s)
AssignCellsToSamples
### Affected version(s)
- [X] Latest public release version [Version:2.5.1(680c2ea_1642084299)]
### Description
This might not be a bug, but I can…
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home/testing tools/PsyOPS$ python PsyOPS.py --GWAS-hit-file Howard_102_MDD.tsv --output-file PsyOPS_Clust2_MDD.tsv
Loaded 102 autosomal GWAS hits from Howard_102_MDD.tsv
TypeError: unhashable type: …
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I'd like to get the GCViT instances linked from the tools menu.
Since we have four instances (and there will likely be more coming), I am thinking that we should have a landing page for them - mayb…
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Hi,
Some GWAS tools like plink2 recommend running with multiple phenotypes at once rather than multiple runs of single phenotypes.
> If you have multiple quantitative phenotypes with either no missi…
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## 1. Bug description
I run the example, it success, but when it plot, it throw "Error in dplyr::**slice_max**(., order_by = c(symbol, width), n = max_transcripts"
Problem while computing indices.
…