User: Rubal

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Rubal210
Reputation:
210
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Location:
Germany
Last seen:
5 months, 1 week ago
Joined:
7 years, 6 months ago
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Posts by Rubal

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Comment: C: VCF input for KaryotypeR
... Thanks the code. When I try with this commandL kpPlotRainfall(kp, data = tmp.vcf.data , col=variant.colors) I get the error: Error in attr(x, "tsp") <- c(1, NROW(x), 1) : attempt to set an attribute on NULL I suspect this is related to needing to create a correct contig base plot for adding th ...
written 5 months ago by Rubal210
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Comment: C: VCF input for KaryotypeR
... OK I just added some of it as there are >1000 lines for header due to a large number of contigs ...
written 5 months ago by Rubal210
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Comment: C: VCF input for KaryotypeR
... substantially modified the post for readability and will do this thanks ...
written 5 months ago by Rubal210
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Comment: C: VCF input for KaryotypeR
... Thanks for the help but 'start' is a column of integer values in my table. I think I am inappropriately using the toGranges() function. I feel there must be a straightforward way to convert a vcf to a granges object suitable for karyotypeR and was just wondering if someone could point me to that. ...
written 5 months ago by Rubal210
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Comment: C: VCF input for KaryotypeR
... Thanks for the reply. The data I give is an alternative format encase that is easier to work with for karyotypeR. I've amended the answer with an example vcf row and example error ...
written 5 months ago by Rubal210
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VCF input for KaryotypeR
... Hello Everyone, I am trying to use the R package KaryotypeR to produce rainfall plots in R. I am having trouble reading my VCF data into R and getting it to work in KaryotypeR. I've got their tutorial to work (link here): [https://bernatgel.github.io/karyoploter_tutorial//Examples/Rainfall/Rainfal ...
R written 5 months ago by Rubal210 • updated 5 months ago by Bastien Hervé3.7k
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Calculate Mean absolute allele frequency difference from MS output
... Does anyone know of a tool that can take MS coalescent simulator output format as input and calculate the mean absolute allele frequency different between two populations for the simulated loci? I've simulated 100 10kb regions of two divergent populations and would like to calculate the absolute a ...
simulations allele frequency ms written 13 months ago by Rubal210
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Comment: C: Are there tools to visually model/simulate the spread of a mutant cell populatio
... thanks I'll take a look! ...
written 2.4 years ago by Rubal210
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Are there tools to visually model/simulate the spread of a mutant cell population in 2D?
... Hello Everyone, I want to model growth in a colony of cells on a 2D surface. I want to see how a mutant cell appears that appears at time X has a growth rate X times greater than other cells in the culture, how it will spread over a 2D surface competing with the original cells. Are there any tools ...
simulations cells written 2.5 years ago by Rubal210 • updated 2.5 years ago by Jean-Karim Heriche18k
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Comment: C: Calculating statistical significance of overlap between two groups of genes - ad
... great this works. Thanks a lot! I have 10 lists and want to do all pairwise comparisons between them. I would plan to reasign geneListA ,geneListB, gA and gB each time and rerun this. Is there a much more efficient way? Don't worry if not, I'm happy to do it this way. Thanks again ...
written 2.5 years ago by Rubal210

Latest awards to Rubal

Great Question 9 months ago, created a question with more than 5,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 9 months ago, created a question with more than 1,000 views. For Identifying which allele is derived in non-human species
Popular Question 9 months ago, created a question with more than 1,000 views. For Best way to compare rate of amino acid change between proteins?
Popular Question 10 months ago, created a question with more than 1,000 views. For How to compare the rate of sequence or amino acid evolution between a set of genes?
Popular Question 24 months ago, created a question with more than 1,000 views. For How to compare the rate of sequence or amino acid evolution between a set of genes?
Popular Question 24 months ago, created a question with more than 1,000 views. For How Can I Divide Snp Data Into Fixed Windows Based On Physical Distance ?
Popular Question 24 months ago, created a question with more than 1,000 views. For Where To Find A Good Estimate Of The Background Mutation Rate In Rattus Norvegicus
Popular Question 24 months ago, created a question with more than 1,000 views. For Interpreting XPEHH output
Student 24 months ago, asked a question with at least 3 up-votes. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Supporter 2.4 years ago, voted at least 25 times.
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Interpreting XPEHH output
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Overlap between 2 sets of genomic regions of differing size
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Detect Regions In A List That Are Within 1 Megabase Of Each Other
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Where To Find A Good Estimate Of The Background Mutation Rate In Rattus Norvegicus
Popular Question 3.4 years ago, created a question with more than 1,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 4.1 years ago, created a question with more than 1,000 views. For Where To Find A Good Estimate Of The Background Mutation Rate In Rattus Norvegicus
Student 4.1 years ago, asked a question with at least 3 up-votes. For How To Identify Substitutions Between Populations In A Vcf
Popular Question 4.8 years ago, created a question with more than 1,000 views. For Where To Find A Good Estimate Of The Background Mutation Rate In Rattus Norvegicus

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