User: s.w.vanderlaan

Reputation:
40
Status:
New User
Location:
Netherlands
Website:
http://www.atheroexpre...
Twitter:
swvanderlaan
Last seen:
7 months, 3 weeks ago
Joined:
4 years, 4 months ago
Email:
s*************@gmail.com

Posts by s.w.vanderlaan

<prev • 14 results • page 1 of 2 • next >
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Comment: C: How to use 1000 Genomes data for LDheatmap package in R
... Did you ever fix this? ...
written 7 months ago by s.w.vanderlaan40
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Comment: C: LDheatmap with custom genome
... Did you ever fix this? ...
written 7 months ago by s.w.vanderlaan40
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What is the effect size in output of FaST-LMM when using EWASher?
... Hi, Perhaps a naive question, but it's just not clear to me. From the adapted FaST-LMM program EWASher I get this output. SNP Chromosome GeneticDistance Position Pvalue Qvalue N NullLogLike AltLogLike SnpWeight SnpWeightSE OddsRatio WaldStat NullBias NullCov00Weight NullCov01Weight ...
fast-lmm ewasher written 2.1 years ago by s.w.vanderlaan40 • updated 2.1 years ago by genomax70k
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Comment: C: Add GenomicRanges to SummarizedExperiment
... I did, here's what I get. > rowRanges(RAW_DESeq2A) > GRangesList object of length 63677: > $ENSG00000000003 > GRanges object with 0 ranges and 0 metadata columns: > seqnames ranges strand > > > $ENSG00000000005 > GRan ...
written 2.6 years ago by s.w.vanderlaan40 • updated 2.2 years ago by WouterDeCoster40k
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Comment: C: Add GenomicRanges to SummarizedExperiment
... I know. But the point is: these genomic ranges aren't present in my DESeq2 object. Like at all. So how do I get them in manually? ...
written 2.6 years ago by s.w.vanderlaan40
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Comment: C: Snptest (Gen/Sample) Files To R
... Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit. ...
written 2.6 years ago by s.w.vanderlaan40
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Comment: C: Snptest (Gen/Sample) Files To R
... Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit. ...
written 2.6 years ago by s.w.vanderlaan40
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Comment: C: Snptest (Gen/Sample) Files To R
... Just added a link to our GWASToolKit on GitHub: https://github.com/swvanderlaan/GWASToolKit. ...
written 2.6 years ago by s.w.vanderlaan40
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Add GenomicRanges to SummarizedExperiment
... Hi, I've got RNAseq data which was processed and given to me in a text-file. The rows are EnsemblIDs, and the columns the individuals with their counts. I've loaded these data, and ran DESeq2. Now I want to plot the log2 fold changes similar as is explained here: http://www.bioconductor.org/help/w ...
deseq2 summarizedexperiment granges written 2.6 years ago by s.w.vanderlaan40 • updated 2.2 years ago by WouterDeCoster40k
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Answer: A: 450k CpG methylation to functional annotation
... Can't you just use the annotation file from Illumina? ...
written 3.4 years ago by s.w.vanderlaan40

Latest awards to s.w.vanderlaan

Popular Question 13 months ago, created a question with more than 1,000 views. For Add GenomicRanges to SummarizedExperiment
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Correlation-heatmap alongside a protein level heatmap

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