User: vinvan

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vinvan40
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Posts by vinvan

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Answer: A: Scaling Data error on Seurat
... Does setting `display.progress = FALSE` instead of `display.progress = F` help? Looks like you might have defined F already before this... ...
written 5 weeks ago by vinvan40
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Answer: A: TCGA Broad GDAC Firehose Parse and Match
... There are quite a few R packages out there that do exactly this. You can check [TCGABiolinks][1] or [TCGA2STAT][2]. [1]: http://www.bioconductor.org/packages/release/bioc/html/TCGAbiolinks.html [2]: https://cran.r-project.org/web/packages/TCGA2STAT/index.html ...
written 10 months ago by vinvan40
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Comment: C: Database of phosphatase targets
... Yes, but that one does not seem to contain the substrates? ...
written 10 months ago by vinvan40
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Database of phosphatase targets
... Does anybody know of a reliable database of phosphates and their (putative) targets? I found [DEPOD][1] but was wondering whether there are more around. Thanks! [1]: http://depod.bioss.uni-freiburg.de/index.php ...
phospatase written 10 months ago by vinvan40 • updated 10 months ago by arta540
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vcftools --freq output always zero
... Hello, I'm trying to quantify the frequency of alleles at specific locations in a bam file generated by Samtools pileup using the command: samtools mpileup -l positions.bed -uvf ref.fa -R in.bam | vcftools --vcf - --freq The output of this returns a frequency of zero for each allele (even the ...
allele vcftools written 10 months ago by vinvan40 • updated 10 months ago by Kevin Blighe33k
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Comment: C: How to produce a unimodal distribution of genes expressed genes
... I modified my answer slightly for clarity. 1) run the plot and lines commands in succession; lines can be used to overlay a plot 2) I would suggest to read the manual of the density command with `?density` in R ...
written 11 months ago by vinvan40
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Answer: A: How to produce a unimodal distribution of genes expressed genes
... As far as I know there is no *golden standard* when it comes to determining a cutoff value. Moreover, depending on the goal of your experiment you might not want to discard the genes which are lowly expressed. If you would like to apply a cutoff, I would suggest making the density plots and see whet ...
written 11 months ago by vinvan40
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Variant calling on single-cell data
... As part of a study on cancer relapse upon treatment, we performed single cell RNAseq and single cell DNA seq on primary tumor tissue before treatment and after relapse. Now, my collaborators would like to know whether certain variants that are present in a set of cancer driving genes in the relapsed ...
single-cell variant snp written 11 months ago by vinvan40 • updated 7 months ago by oneillkza70

Latest awards to vinvan

Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Scaling Data error on Seurat
Scholar 5 weeks ago, created an answer that has been accepted. For A: Scaling Data error on Seurat

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