User: bernatgel

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bernatgel1.8k
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Posts by bernatgel

<prev • 99 results • page 1 of 10 • next >
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Answer: A: coverage plot for all chromosomes
... You can use [karyoploteR](http://bioconductor.org/packages/release/bioc/html/karyoploteR.html) as Bastien suggested, but if you can a whole genome coverage plot I think the best approach would be to perform a bit of preprocessing instead of going directly to `kpPlotCoverage`. I would recommend usi ...
written 10 days ago by bernatgel1.8k
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Comment: C: Plotting overlapping genomic segments in R
... It should run without any problem... it's been available for the last few Bioconductor releases. Did you try with BiocManager::install("karyoploteR")? Since it's a Bioconductor package it cannot be installed with `install.packages()` but with `BiocInstaller::install()`. You have the exact code at th ...
written 12 days ago by bernatgel1.8k
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Answer: A: Plotting overlapping genomic segments in R
... If you want to plot them, you can use [karyoploteR](http://bioconductor.org/packages/karyoploteR/). The function [kpPlotRegions](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotRegions/PlotRegions.html) plot the regions non-overlapping by default and will create the plot I think you a ...
written 13 days ago by bernatgel1.8k
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Comment: C: How to do survival analysis?
... I agree with the answer but I would just add that you need to take into account multiple testing! If you are testing all genes to see if they correlate with survival you are doing 20k hypothesis tests. You need the probability of finding something "statistically significant" just by chance without a ...
written 15 days ago by bernatgel1.8k
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Comment: C: Cannot identify software used to make image
... If you have R installed, it should be fairly easy to install. if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("karyoploteR", version = "3.8") If you need more than this, feel free to ask. BTW, to run this exact code you will need ...
written 28 days ago by bernatgel1.8k
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Answer: A: Cannot identify software used to make image
... I don't know the exact software used to create that image but you can reproduce it using [karyoploteR]( http://bioconductor.org/packages/karyoploteR/). ![reproduction of the DMR plot using karyoploteR][1] Here's the code. We start creating random regions on the genome with [regioneR](http://biocon ...
written 4 weeks ago by bernatgel1.8k
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Answer: A: convert bed file to GRangeList object
... The function `toGRanges` from package [regioneR](http://bioconductor.org/packages/regioneR/) will work both with a data frame or a file with a bed-like structure (it will internally call rtracklayer::import used by igor to actually import the data) library(regioneR) dd <- toGRanges("d ...
written 4 weeks ago by bernatgel1.8k
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Comment: C: Visualizing CNV data based from bed or bedgraph format
... Sure, to have all chromosomes in one line use kp <- plotKaryotype(plot.type=4) and keep everything else the same. There are various plot types available to choose from. You can find them in [the tutorial page](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotTypes/PlotTypes.ht ...
written 5 weeks ago by bernatgel1.8k
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Answer: A: Visualizing CNV data based from bed or bedgraph format
... Hi sm.hasehmin, You can use the Bioconductor package [karyoploteR](http://bioconductor.org/packages/karyoploteR/) for this. You can plot the data as points using [kpPoints](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/Points/Points.html) as in the example below or you could change tha ...
written 5 weeks ago by bernatgel1.8k
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Answer: A: R, how to retrieve the genes associated to a VCF file?
... If you want to know what genes are affected by the variants in the VCF file what you should do is **annotate** the VCF. There are many tools for that and wouldn't recommend doing that with your own code. For example - [Annovar](http://annovar.openbioinformatics.org/en/latest/) - [VEP](https://www. ...
written 7 weeks ago by bernatgel1.8k

Latest awards to bernatgel

Good Answer 25 days 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
Scholar 25 days ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 4 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 5 weeks ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 6 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
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 10 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 10 weeks ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 3 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
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
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 3 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Scholar 5 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Teacher 12 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
Guru 16 months ago, received more than 100 upvotes.
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
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

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