User: ceruleanivy

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ceruleanivy20
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Posts by ceruleanivy

<prev • 34 results • page 1 of 4 • next >
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Distance matrix based on mutation rates
... I would like to calculate the phylogenetic distance between 500 patients' breast cancer subtypes and need help when it comes to the right method for producing distance matrices. My patients are equally divided between the 5 sub-types (100 each) and the number of variables represents the number of po ...
software error genome next-gen written 19 hours ago by ceruleanivy20 • updated 15 hours ago by cyinbox0
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Comment: C: Statistical significance in phylogenies
... Thanks, do you know which function will give the me the lowest possible p value between two species ? For example in a population of 10 that will eventually lead to a 10x10 matrix of p values. ...
written 9 days ago by ceruleanivy20
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Comment: C: Statistical significance in phylogenies
... I think you got it correct, I would like to receive some sort of metric to help me quantify the relationship between two species in the context of statistical significance. ...
written 10 days ago by ceruleanivy20
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Statistical significance in phylogenies
... I have constructed a distance matrix in order to produce a phylogenetic tree for 10 species in R package 'phangorn' and I would like to know how can I calculate p-values for significantly different species based purely on phylogenetic data. I would appreciate some insight, especially by the ones who ...
genome R next-gen written 10 days ago by ceruleanivy20 • updated 10 days ago by Manvendra Singh1.8k
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VisCap 'mat.cov' not found error in R
... I am using VisCap (https://github.com/pughlab/VisCap/wiki) in order to conclude copy number variations by reading BAM files created from Ion Torrent next-generation sequencing on FFPE tumor samples. After successfully creating the required output from the GATK DepthOfCoverage tool and running VisCap ...
software error R next-gen written 18 days ago by ceruleanivy20
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Infer CNVs from SNP variant allele fractions
... I am currently working on data obtained from proton sequencing (IonTorrent) on bulk tumor micro FFPE samples, using panels for exome targeting. Although I've came across some literature on that issue I am not quite experienced so I would like to ask what are the most popular algorithms/software on i ...
R next-gen snp written 4 weeks ago by ceruleanivy20 • updated 27 days ago by willgilks140
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Comment: C: Searching for ClinVar entries based on SNP annotation
... I would prefer a more automated method (programming based) that takes advantage of the latest database entries. If /tab_delimited/archive/ are the files you are referring to then I will probably have to download and decompress/merge every .gz every time I want to update my database of clinvar entrie ...
written 7 months ago by ceruleanivy20
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Searching for ClinVar entries based on SNP annotation
... I currently have a table for every patient with all of their variants on exome sequencing. One column contains the identified dbsnp code (rs). I would like to know how can I automatically generate another column that stores the ClinVar information for every available common single nucleotide polymor ...
genome R snp written 7 months ago by ceruleanivy20 • updated 7 months ago by Newgene200
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Mutation annotation on tumor phylogenetic trees
... I have binary matrices with mutation presence absence for every patient where the first column contains an identifier for the mutation. So far, I have produced several phylogenetic trees with phangorn, however, the option of depicting common and private mutations above each branch is not available. ...
gene R next-gen snp sequencing written 8 months ago by ceruleanivy20
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Simple chord diagram depicting amino acid change
... I'm new to packages like 'circos' and 'circlize' and cannot figure out how to create a simple chord diagram showing amino acid changes in missense mutations. The circle is divided into two equal arcs (reference and altered) and each of them should contain three categories (polar, hydrophobic, charge ...
R written 8 months ago by ceruleanivy20

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