User: Floris Brenk

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Floris Brenk790
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USA
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Posts by Floris Brenk

<prev • 173 results • page 1 of 18 • next >
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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 9 weeks ago by Floris Brenk790 • updated 9 weeks ago by cmdcolin700
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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 3 months ago by Floris Brenk790
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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 3 months ago by Floris Brenk790
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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 3 months ago by Floris Brenk790 • updated 3 months ago by Devon Ryan74k
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Comment: C: How to make a nice mutation overview figure like this?
... Also very nice thanks! ...
written 4 months ago by Floris Brenk790
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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 4 months ago by Floris Brenk790
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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 4 months ago by Floris Brenk790
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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 4 months ago by Floris Brenk790
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PCA matching controls with cases using genotypes
... Hi there, I have a relatively small dataset of cases (n=~800) and a very large amount of controls (n=~8000) in plink format. Now I would like to have the case-control ration 1:3 for further analysis. I was wondering is there a method or are there scripts available that perform some kind of PCA matc ...
pca plink written 5 months ago by Floris Brenk790
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Answer: A: Duplicate ID in bed file
... Using --list-duplicate-vars you can identify the duplicates in the data [plink website identifying duplicates][1] And using --exlcude you can remove your snps [plink website removing snps][2] [1]: https://www.cog-genomics.org/plink/1.9/data#list_duplicate_vars [2]: https://www.cog-genomics.or ...
written 5 months ago by Floris Brenk790

Latest awards to Floris Brenk

Popular Question 9 weeks ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Popular Question 3 months ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Scholar 4 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 6 months ago, created a question with more than 1,000 views. For Coverage plots of gvcf files
Popular Question 10 months ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Scholar 11 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Student 14 months ago, asked a question with at least 3 up-votes. For Reformat minimac imputated files to plink file
Voter 15 months ago, voted more than 100 times.
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Difference Between Gene Expression And Transcript Expression
Scholar 17 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Scholar 18 months ago, created an answer that has been accepted. For A: What's the best way to map CAGE-seq data to the genome?
Centurion 20 months ago, created 100 posts.
Scholar 20 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 21 months ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Appreciated 22 months ago, created a post with more than 5 votes. For A: Difference Between Gene Expression And Transcript Expression
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Snp Coordinates Hg19, Hg18, Hg17 Changed But Also Closest Genes Etc
Popular Question 2.3 years ago, created a question with more than 1,000 views. For SNP in Transcription factor binding site analysis
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Identify The Effect Of Covariates With Count Data

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