User: Floris Brenk

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Floris Brenk890
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USA
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3 months, 3 weeks ago
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5 years, 9 months ago
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Posts by Floris Brenk

<prev • 175 results • page 1 of 18 • next >
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Epistasis in GWAS loci, examples?
... Hi all, I was been working on epistasis in a couple of GWAS loci. Basically the theory is that some GWAS loci might not work in an additive manner, but more in an epistasic way and calculated this using R : Formula <- formula(paste("pheno ~ PC1 + PC2 + PC3 + PC4 + PC5 + SEX + SNP1 * SNP2")) ...
epistasis gwas R written 6 months ago by Floris Brenk890
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Rare variant meta-analyzing tests
... Hi all, I have 5 different (dosage VCF files, with both continuous and binary phenotypes) datasets and I'm trying to meta-analyze rare variants in each dataset. Ideally I would like to group the variants per gene and then meta-analyze the p-values per gene from all 5 datasets, but I haven't found a ...
meta analyze rare variants written 19 months ago by Floris Brenk890 • updated 4 months ago by swetansu0
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Add gene annotation/information to CNV plot in R
... Hi all, Im have a few interesting (genotyping) CNVs and now I want to plot them using the B allele frequency and LogR ratio. There are already several topics about this [for example here][1], but ideally I am more looking for something like pennCNV plots but then with gene annotation on the x-axis ...
R cnv plot written 22 months ago by Floris Brenk890 • updated 22 months ago by cmdcolin1.2k
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Comment: C: ATACseq and HiC sequencing
... Great thanks all for your help, much appreciated! Got one more additional questions, is there any need to PhiX spike-in during HiC or ATAC sequencing? or can the libraries just go on hiseq without issues? ...
written 23 months ago by Floris Brenk890
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Comment: C: ATACseq and HiC sequencing
... Was thinking about this method [HiC2][1] Very clear paper and protocol but no guidelines on sequencing depth... Just one sentence "Datasets from Rao et al. were selected solely based on their read depth that was comparable to datasets obtained with Hi-C 2.0 (100–200 million reads)" [1]: https://w ...
written 23 months ago by Floris Brenk890
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ATACseq and HiC sequencing
... Hi there, We are looking into ATACseq and HiC sequencing of some human derived samples. Does anyone has any recommendation about sequencing depth? e.g. how many samples to pool per lane on Illumina HiSeq. Have been looking around but no real data is present on this. Also is there some best practice ...
atac hic written 23 months ago by Floris Brenk890 • updated 23 months ago by Devon Ryan92k
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Comment: C: How to make a nice mutation overview figure like this?
... Also very nice thanks! ...
written 2.1 years ago by Floris Brenk890
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Answer: A: How to make a nice mutation overview figure like this?
... In the end I think this is the easiest way -> [Lollipops][1] [1]: https://github.com/pbnjay/lollipops ...
written 2.1 years ago by Floris Brenk890
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Comment: C: How to make a nice mutation overview figure like this?
... Looks very pretty and interesting thanks! I only have ~50 mutations per gene so I think the circos plot is a bit too complicated to show for those genes... ...
written 2.1 years ago by Floris Brenk890
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How to make a nice mutation overview figure like this?
... Hi all, Does anyone know how to make a nice mutation overview figure like this [nice figure][1]? I found a similar way to make these plots with [GenVisR][2] But was curious whether there are also other packages out there? Thanks Floris [1]: http://jamanetwork.com/data/Journals/NEUR/935945/nbs1 ...
R written 2.1 years ago by Floris Brenk890

Latest awards to Floris Brenk

Popular Question 6 months ago, created a question with more than 1,000 views. For Covariates... what to do with them and how to handle them?
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Popular Question 23 months ago, created a question with more than 1,000 views. For Coverage plots of gvcf files

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