User: Floris Brenk

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Floris Brenk900
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USA
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6 years, 2 months ago
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Posts by Floris Brenk

<prev • 176 results • page 1 of 18 • next >
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chromosome X and Y GWAS results
... Dear all, I was wondering whether anyone knows of any robust GWAS loci on chromosome X and Y? Have been looking around a bit but haven't found much yet. Specifically curious whether there are differences in risk between male and females with risk variants are present on X. Thanks all! ...
gwas X Y written 9 weeks ago by Floris Brenk900
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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 11 months ago by Floris Brenk900
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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 2.0 years ago by Floris Brenk900 • updated 8 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 2.3 years ago by Floris Brenk900 • updated 2.3 years ago by cmdcolin1.3k
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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 2.3 years ago by Floris Brenk900
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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 2.4 years ago by Floris Brenk900
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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 2.4 years ago by Floris Brenk900 • updated 2.4 years ago by Devon Ryan94k
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Comment: C: How to make a nice mutation overview figure like this?
... Also very nice thanks! ...
written 2.5 years ago by Floris Brenk900
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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 2.5 years ago by Floris Brenk900
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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 2.5 years ago by Floris Brenk900

Latest awards to Floris Brenk

Popular Question 6 weeks ago, created a question with more than 1,000 views. For Coverage/Read Depth per SNP in 1000Genomes
Popular Question 8 months ago, created a question with more than 1,000 views. For RNA-seq de novo transcript assembly from one gene
Popular Question 8 months ago, created a question with more than 1,000 views. For Covariates... what to do with them and how to handle them?
Scholar 8 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Popular Question 8 months ago, created a question with more than 1,000 views. For creating chr17 haplotypes h1 and h2 from exome / gwas data
Popular Question 8 months ago, created a question with more than 1,000 views. For Assigning haplotypes to individuals
Student 11 months ago, asked a question with at least 3 up-votes. For Imputation of chromosome X using the Michigan imputation server
Popular Question 11 months ago, created a question with more than 1,000 views. For Assigning haplotypes to individuals
Popular Question 11 months ago, created a question with more than 1,000 views. For Covariates... what to do with them and how to handle them?
Popular Question 11 months ago, created a question with more than 1,000 views. For RNA-seq de novo transcript assembly from one gene
Popular Question 11 months ago, created a question with more than 1,000 views. For Looking for a whole genome sequencing analysis course
Popular Question 17 months ago, created a question with more than 1,000 views. For Looking for a whole genome sequencing analysis course
Great Question 17 months ago, created a question with more than 5,000 views. For r2 correlation interpretation snp in plink pruning
Popular Question 17 months ago, created a question with more than 1,000 views. For Covariates... what to do with them and how to handle them?
Great Question 17 months ago, created a question with more than 5,000 views. For Reformat minimac imputated files to plink file
Popular Question 17 months ago, created a question with more than 1,000 views. For creating chr17 haplotypes h1 and h2 from exome / gwas data
Popular Question 17 months ago, created a question with more than 1,000 views. For Pre-calculated Ka/Ks ratio per gene of human genome
Popular Question 17 months ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Popular Question 17 months ago, created a question with more than 1,000 views. For Conservation score for a piece of human genome
Popular Question 17 months ago, created a question with more than 1,000 views. For Looking for a whole genome sequencing analysis course
Popular Question 21 months ago, created a question with more than 1,000 views. For Trimming Fastq File Based On First Nucleotide
Popular Question 21 months ago, created a question with more than 1,000 views. For Pre-calculated Ka/Ks ratio per gene of human genome
Popular Question 21 months ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Popular Question 21 months ago, created a question with more than 1,000 views. For Conservation score for a piece of human genome
Popular Question 21 months ago, created a question with more than 1,000 views. For Looking for a whole genome sequencing analysis course

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