User: ceruleanivy

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ceruleanivy30
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3 weeks, 4 days ago
Joined:
2 years, 11 months ago
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c**********@hotmail.com

Posts by ceruleanivy

<prev • 39 results • page 1 of 4 • next >
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What are the available automated microscopy options in 2018?
... I know this is not a pure bioinformatics question but my lab has been researching methods of obtaining large amounts of image sets automatically in order to extract useful histological features out of them and correlate with sequencing data. You may find similar work there https://arxiv.org/abs ...
microscopy snp written 11 weeks ago by ceruleanivy30 • updated 14 days ago by Biostar ♦♦ 20
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Comment: C: SNP tools to infer copy number variations (CNVs)
... Thanks for the response. I have targeted ampliseq NGS data on DNA from FFPE samples on ~400 amplicons. I don't have any other genetic data on these patients. The panel was designed with respect to regions that contain many informative SNPs for inferring zygosity. ...
written 21 months ago by ceruleanivy30
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SNP tools to infer copy number variations (CNVs)
... I have tried nearly every method regarding the extrapolation of different CNVs by utilizing data from coverage and reads on NGS settings, but unfortunately end up with unreliable results (too much variance among log2s to be considered trustworthy). I would like to know what tool is best for methods ...
R next-gen sequencing written 21 months ago by ceruleanivy30 • updated 21 months ago by Vincent Laufer1.0k
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Comment: C: Different reference and variant allele in IonTorrent variantCaller
... Thanks for your response. Although I use ionReporter for annotation, I recently decided to switch to annovar and I have to admit that I've never looked up the VCF Processing Guide on the website. From my understanding of it, I should perhaps drop the VCF columns and also consider removing some varia ...
written 22 months ago by ceruleanivy30
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Different reference and variant allele in IonTorrent variantCaller
... I am doing a targeted amplicon NGS analysis on cholangiocarcinoma FFPE samples on proton sequencer on a run with 88% ISP loading. The XLS file provided, containing all the barcodes that went into analysis with the variantCaller (v5.0.2.1) software in IonServer has two different columns for reference ...
next-gen sequence sequencing written 22 months ago by ceruleanivy30 • updated 22 months ago by geocarvalho80
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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 24 months ago by ceruleanivy30 • updated 24 months ago by genebow140
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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 2.0 years ago by ceruleanivy30
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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 2.0 years ago by ceruleanivy30
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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 2.0 years ago by ceruleanivy30 • updated 2.0 years ago by Manvendra Singh2.0k
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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 2.0 years ago by ceruleanivy30 • updated 11 months ago by nkausthu20

Latest awards to ceruleanivy

Popular Question 21 months ago, created a question with more than 1,000 views. For Infer loss of heterozygosity from SNP variant frequencies
Popular Question 21 months ago, created a question with more than 1,000 views. For Download all DNA mutations from TCGA
Popular Question 21 months ago, created a question with more than 1,000 views. For Tumor phylogenetic tree software
Popular Question 21 months ago, created a question with more than 1,000 views. For Only one cluster in multiple tumor phylogeny samples
Popular Question 21 months ago, created a question with more than 1,000 views. For Detecting Loss of Heterozygosity in tumors
Popular Question 21 months ago, created a question with more than 1,000 views. For Searching for ClinVar entries based on SNP annotation

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