User: bernatgel
bernatgel • 2.9k
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Posts by bernatgel
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... Hi adily,
Happy karyoploteR worked for you.
For gene plotting I'm developing a new package, genoploteR, based on karyoploteR, but it's not yet finished. You can take a look at it at [https://github.com/bernatgel/genoploteR]. It can currently plot the gene (with tuneable intron compression) and a ...
written 15 days ago by
bernatgel • 2.9k
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Comment:
C: Heatmaps with R for GC content
... Hi,
It's not currently possible to assign different colors to different values. Internally it uses colorRamp to interpolate between the given colors so the options are limited. You can, however, influence the color assignment by specifying the colors. For example, if instead of `c("blue", white", " ...
written 18 days ago by
bernatgel • 2.9k
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... Hi Charles G,
You could use the Bioconductor package [karyoploteR](https://bioconductor.org/packages/karyoploteR/) for this. It has a function (`kpHeatmap`) for plots like this.
In this example I'm just using random numbers, but you can read the bed file with
gc.cont <- toGRanges("my_bed ...
written 23 days ago by
bernatgel • 2.9k
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... The Linux system in my institution have several R versions and several Rstudio versions running in parallel. This is managed by the SysAdmin, but I think it's "simply" a question of installing them on different directories. In addition, I'm pretty sure you can set an environment variable before star ...
written 26 days ago by
bernatgel • 2.9k
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... You should be able to plot the ROH using [karyoploteR](https://bioconductor.org/packages/karyoploteR/). You can find information on how to use it on the vignette and a tutorial and some more complex examples with step by step instructions at [https://bernatgel.github.io/karyoploter_tutorial/].
It m ...
written 4 weeks ago by
bernatgel • 2.9k
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2
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112
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... and load the BAM file in there (maybe the VCF too so you can easily fin the variant you want), but the BAM will give you the pileup ...
written 5 weeks ago by
bernatgel • 2.9k
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152
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... For genes (exons, introns, promoters, UTRs...) if you are using R and working on human or a fairly common model organism, you can use Bioconductor's TxDb objects. For example [TxDb.Hsapiens.UCSC.hg38.knownGene](https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/) for human or [TxDb. ...
written 7 weeks ago by
bernatgel • 2.9k
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... Hi,
You can use the `getSeq` and `alphabetFrequency` functions from Bioconductor's [Biostrings](https://bioconductor.org/packages/Biostrings/) package to obtain the sequence and compute the frequency of each nucleotide, and then, just divide the sum of G+C by the total number of nucleotides.
To us ...
written 11 weeks ago by
bernatgel • 2.9k
1
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140
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... If it's cancer samples, you can try with ASCAT, if it's germline data, then maybe DNAcopy or GenoCN? ...
written 12 weeks ago by
bernatgel • 2.9k
1
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1
answer
140
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1
answers
... If you have a file for each sample, you can use the R/Bioconductor package [CopyNumberPlots]( https://bioconductor.org/packages/CopyNumberPlots/) to create plots of your raw data and if you call copy number variants (with PennCNV or any other) you can also plot the calls along your data.
...
written 12 weeks ago by
bernatgel • 2.9k
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For Scientific Programmer for Translational Bioinformatics of Hereditary Cancer at the IMPPC, Badalona, Barcelona, Spain
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