User: Rubal

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Rubal220
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Germany
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7 years, 8 months ago
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Posts by Rubal

<prev • 85 results • page 2 of 9 • next >
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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 7 months ago by Rubal220 • updated 7 months ago by Bastien Hervé4.2k
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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 15 months ago by Rubal220
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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 2.6 years ago by Rubal220
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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 2.6 years ago by Rubal220 • updated 2.6 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 2.7 years ago by Rubal220
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Comment: C: Calculating statistical significance of overlap between two groups of genes - ad
... do you have any idea what might be causing this error? I checked that all the input files are present and correct. ...
written 2.7 years ago by Rubal220
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Comment: C: Calculating statistical significance of overlap between two groups of genes - ad
... just to confirm, I think for the line starting 'gBsim <-' you mean to sample from geneListB not geneListA correct? Also , for the subsampling section I get the error: Error in FUN(X[[i]], ...) : unused argument (X[[i]]) Trying to troubleshoot it now ...
written 2.7 years ago by Rubal220
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Comment: C: Calculating statistical significance of overlap between two groups of genes - ad
... Good thought, though this is for genomic analyses of DNA not RNA, so I have to include the entire genomic background as in theory any gene could appear. I think all sets are exposed to the same underlying biases that might results in a base level of sharing that is above the amount seen from random ...
written 2.7 years ago by Rubal220
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Comment: C: Calculating statistical significance of overlap between two groups of genes - ad
... I completely agree, just meant that R reports it as 0 but ofcourse you can only say it's smaller than your number of iterations. ...
written 2.7 years ago by Rubal220
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Comment: C: Calculating statistical significance of overlap between two groups of genes - ad
... One issue I have is that for some lists the sampling overlap is never as high as the observed overlap, so P-values are reported as 0. I would still like a way to assess whether some lists have a lot more sharing compared to random sampling than others. For example if in some cases up to 50% of genes ...
written 2.7 years ago by Rubal220

Latest awards to Rubal

Popular Question 7 months ago, created a question with more than 1,000 views. For Identifying which allele is derived in non-human species
Great Question 11 months ago, created a question with more than 5,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 11 months ago, created a question with more than 1,000 views. For Identifying which allele is derived in non-human species
Popular Question 11 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 12 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 2.1 years 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 2.1 years 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 2.1 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
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Interpreting XPEHH output
Student 2.1 years ago, asked a question with at least 3 up-votes. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Supporter 2.6 years ago, voted at least 25 times.
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Interpreting XPEHH output
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Overlap between 2 sets of genomic regions of differing size
Popular Question 3.3 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 3.3 years ago, created a question with more than 1,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 3.6 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 3.6 years ago, created a question with more than 1,000 views. For Summarising Whole Genome Allele Frequency Spectrum from VCF file
Popular Question 4.3 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 4.3 years ago, asked a question with at least 3 up-votes. For How To Identify Substitutions Between Populations In A Vcf
Popular Question 5.0 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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