User: bernatgel

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bernatgel2.9k
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Posts by bernatgel

<prev • 177 results • page 1 of 18 • next >
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Comment: C: ROH-script for graphical visualization in R
... 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 bernatgel2.9k
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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 bernatgel2.9k
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Answer: A: Heatmaps with R for GC content
... 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 bernatgel2.9k
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Answer: A: Is there other IDE like R studio working on the linux?
... 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 bernatgel2.9k
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Comment: C: ROH-script for graphical visualization in R
... 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 bernatgel2.9k
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Comment: C: How can I visualize the Pileup to determine if there is a 5 BP deletion?
... 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 bernatgel2.9k
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Comment: C: Genomic position to genomic feature
... 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 bernatgel2.9k
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Answer: A: how to get GC content of multiple ranges in R
... 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 bernatgel2.9k
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Comment: C: Explore CNV data from illumina Array
... 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 bernatgel2.9k
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Answer: A: Explore CNV data from illumina Array
... 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 bernatgel2.9k

Latest awards to bernatgel

Scholar 9 weeks ago, created an answer that has been accepted. For A: How to convert mutation position from gene coordinate to genome coordinate?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to convert mutation position from gene coordinate to genome coordinate?
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: snp density plot
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 8 months ago, created an answer that has been accepted. For A: How to convert mutation position from gene coordinate to genome coordinate?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 11 months ago, created an answer that has been accepted. For A: How to convert mutation position from gene coordinate to genome coordinate?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 16 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Great Question 17 months ago, created a question with more than 5,000 views. For karyoploteR: uncircle your genomes
Scholar 18 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 21 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Centurion 21 months ago, created 100 posts.

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