User: bernatgel

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bernatgel710
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Barcelona, Spain
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@bernatgel
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10 hours ago
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Posts by bernatgel

<prev • 37 results • page 1 of 4 • next >
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Answer: A: Add a legend to circos plot
... As far a I know, there is no functionality in Circos to add labels to tracks. We usually use an external program (Inskscape or similar) to add the labels when preparing the figure to publish. Another option would be to use a text track with the track names, and try to position them as if they were ...
written 16 hours ago by bernatgel710
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Comment: C: How to map SNPs of C. Albicans using custom data?
... I edited the original answer to include some code ...
written 17 hours ago by bernatgel710
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Comment: C: How to map SNPs of C. Albicans using custom data?
... Hi nattzy94, The data in the example is randomly created with `x <- 1:23*10e6` and `y <- rnorm(23, mean=0.5, sd=0.25)`. In your case you would probably read it from a file with the data about your snps (position and frequency). If you can paste here the first lines of your data file I can try ...
written 2 days ago by bernatgel710
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Answer: A: How to map SNPs of C. Albicans using custom data?
... You can use [karyoploteR](https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btx346) to create a plot similar to a manhattan plot and using any genome. To create such plot you should first create an empty plot following [these instructions](https://bernatgel.github.i ...
written 3 days ago by bernatgel710
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Answer: A: CNV detection of single cell genome sequencing
... You can take a look at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069701/ They use a custom approach to CNV calling from single cell data but they provide a good guide and access to code as supplemetary material. Not a full blown package, but it might be helpful. ...
written 7 days ago by bernatgel710
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Answer: A: How to draw the chromosome specific coverage plot using GFF3 file
... Hi @ajaybioinfo, It won't be exactly the same image, but you can get something similar with the R package [karyoploteR](http://bioconductor.org/packages/karyoploteR). 1 - You can create a genome.bed file with the length of your chromosomes and use it to create a plot as in the [Custom Genome](h ...
written 14 days ago by bernatgel710
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Answer: A: Representing A Feature Along The Length Of The Chromosome
... Answering after a few years, in case anyone comes to this question from google et al. You can use [karyoploteR](http://bioconductor.org/packages/karyoploteR/) to plot almost anything on any genome. There are some examples in the [karyoploteR page](https://bernatgel.github.io/karyoploter_tutorial) i ...
written 23 days ago by bernatgel710
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Comment: C: karyoploteR: uncircle your genomes
... Hi @khhgng karyoploteR is only a plotting package and can not help you with the selection and manipulation of your data. If you your genes a in a GRanges object, I would recommend you using the [subsetByOverlaps](https://kasperdanielhansen.github.io/genbioconductor/html/GenomicRanges_GRanges_Usage. ...
written 4 weeks ago by bernatgel710
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Answer: A: how to randomly select intervals of different lengths (not records) from a BED f
... If you can use R, you could use [regioneR]( http://bioconductor.org/packages/regioneR/)'s `createRandomRegions` function to do that. The trick here is to create a mask by subtracting your regions from the whole genome. With that mask the function will select random regions in the only unmasked par ...
written 5 weeks ago by bernatgel710
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Answer: A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
... You can use [karyoploteR](http://bioconductor.org/packages/karyoploteR/) for that. It's a new R/Bioconductor package to plot data on the genome with lots of room for configuration. With karyoploteR you start with an empty plot and keep adding new data iteratively. In your case, we'll use a for loop ...
written 5 weeks ago by bernatgel710

Latest awards to bernatgel

Scholar 14 hours ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Prophet 2 days ago, created a post with more than 20 followers. For karyoploteR: uncircle your genomes
Voter 20 days ago, voted more than 100 times.
Teacher 23 days 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 5 weeks ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 5 weeks ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 5 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
Teacher 5 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 5 weeks ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 5 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
Teacher 4 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 4 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Teacher 4 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 5 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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Good Answer 24 months ago, created an answer that was upvoted at least 5 times. For A: Permutation test with gene size and GC contents
Scholar 24 months ago, created an answer that has been accepted. For A: Permutation test with gene size and GC contents
Appreciated 24 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Teacher 24 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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Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Association between bed files - statistical significance

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