User: bernatgel
bernatgel • 2.7k
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Posts by bernatgel
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... **Link to the offer:** https://idibell.cat/en/ofertes-feina/full-stack-developer-to-incorporate-within-the-eucancan-project/
The global aim of EUCANCan project is to build a network of Personalized Medicine nodes that enables and promotes the generation, exchange and sharing of harmonized and high ...
written 4 days ago by
bernatgel • 2.7k
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Comment:
C: Copy numbers zygosity
... I'd call LOH copy-neutral LOH (CN-LOH) since an heterozygous deletion creates an LOH too. I agree with your definitions of heterozygous and homozygous deletions and have never seen homozygous and heterozygous applied to duplications. >2n for me are gains and define them as 3n, 4n, 5n, 6n... ...
written 14 days ago by
bernatgel • 2.7k
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... You could annotate them with Gene Ontology terms (Cellular Compartment ontology) and check if there are any of the terms related to membrane. Not ideal, but should work. ...
written 14 days ago by
bernatgel • 2.7k
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... Hi mag,
Another option would be to use [karyoploteR](https://bioconductor.org/packages/karyoploteR/) to create your Manhattan plot. The plot will be a bit different since karyoploteR will plot each SNP in its correct position on the genome, by default on hg19 (note that karyoploteR can work with an ...
written 20 days ago by
bernatgel • 2.7k
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... I don't know much about qqman, but this is strange, I think. Are there also squares and circles? or is it an effect of image compression?
In any case, if you want to use another package to plot the manhattan, you can take a look at the karyoploteR tutorial on how to plot manhattan plots ([https://be ...
written 25 days ago by
bernatgel • 2.7k
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... Hi, you might want to take a look at [kpPlotManhattan](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotManhattan/PlotManhattan.html) from [karyoploteR](https://bioconductor.org/packages/karyoploteR/). With it you can create a manhattan plot with correct x coordinates and can plot any ...
written 9 weeks ago by
bernatgel • 2.7k
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Comment:
C: B allele frequency (BAF)
... It should work with other genomes too. And I'm pretty sure it should be possible for it to work with unknown and custom genomes too. ...
written 10 weeks ago by
bernatgel • 2.7k
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Answer:
A: B allele frequency (BAF)
... If you are using R, you can take a look at the [CopyNumberPlots](https://bioconductor.org/packages/CopyNumberPlots/) Bioconductor package. Its focused on generating plots of BAF, LRR and copy-number segments from SNP-array and NGS, but it has a handy function to compute the BAF from a VCF where it w ...
written 10 weeks ago by
bernatgel • 2.7k
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... HI ika,
You can use [karyoploteR]() for this! Instead of plotting the SNPs one after the other equally separated, karyoploteR first creates a base plot with the correct chromosome sizes and then adds data to it. There are multiple functions to add different data types and there's one, [kpPlotManhat ...
written 11 weeks ago by
bernatgel • 2.7k
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... You can also give [karyoploteR](https://bioconductor.org/packages/karyoploteR/) a try.
It has functions to plot peaks, reads densities and many other either in a whole genome view, in a subset of chromosomes or in a local region view.
There's a [karyoploteR tutorial page](https://bernatgel.github. ...
written 12 weeks ago by
bernatgel • 2.7k
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