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Dear Dr John,
I am a PhD student from the University of Cape Town (South Africa). I am working on Staphylococcus aureus genomics in atopic dermatitis. Part of my work includes bacterial-GWAS (pan-…
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Hello,
I am having problems with controlling for the population stuctre in my sample set and I was wodnering if I can get some help? I am not sure when the QQplots are good enough in order to be a…
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Due to old gene symbols used by PheWAS catalog, we see a large number of invalid evidence in the 21.09 release. It raises the question if it make sense to keep this datasource at all considering the s…
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Dear Author
I am trying to apply hogwash to a dataset from Gallibacterium (12 strains) to find associations between SNPs and antibiotic resistance profiles. I have produced the snps, phenotype matr…
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Hello,
I would like to ask whether for a recombination rate adjustments it is necessary to use for example Gubbins before using pyseer or pyseer can take complete care of this issue.
Thank you i…
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myBlink=Blink(Y=myY,GD=myGD,GM=myGM,maxLoop=10,time.cal=T)
[1] "----------------------Welcome to Blink----------------------"
[1] "----------------------Iteration: 1 ----------------------"
[1] "se…
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@tosfos I'd like to filter signatures exported from BugSigDB by review status for #80.
This seems currently not possible as the only column that we have in the export csv files on review status is `R…
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Dear Carl,
Thank you so much for developing this tool. I learned this tool from a paper, and really want to try it with my own data. I want to run association analysis of bacterial SNPs and pheno dat…
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Hi,
I am running the Pangenome Association Study pipeline, following the tutorial guidelines: prokka > panaroo > IQ-tree > pyseer; to estimate a GWAS of presence and absence genes on 4 bacterial grou…