User: Genotepes

gravatar for Genotepes
Genotepes940
Reputation:
940
Status:
Trusted
Location:
Nantes (France)
Last seen:
3 months, 1 week ago
Joined:
8 years, 2 months ago
Email:
c*************@univ-nantes.fr

Doing some statistical genetics - association studies right now and hopefully NGS based association later.. Have worked on T2D and obesity and currently switched to valve diseases and, on a minor mode, arrythmia.

Posts by Genotepes

<prev • 69 results • page 1 of 7 • next >
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Getting intensities using apt-genotype-axiom
... Does anyone know how to get intensities files from `apt-genotype-axiom` used for calling the Affy PMRA chip? Did not find anything in the manuals. Was the `.chp` files with previous version. ...
assembly pmra genotype affymetrix written 3 months ago by Genotepes940 • updated 3 months ago by zx87547.5k
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Comment: C: f3 statistics tutorial or ppt
... Hi thanks for your answer. Yes, I looked (several times I must say) and mainly find papers. I spent like ~30 minutes recently and maybe ~1 hour as a whole. Came across some workshops (http://gaworkshop.readthedocs.io/en/latest/contents/06_f3/f3.html) and papers but nothing looking like a presentatio ...
written 10 months ago by Genotepes940
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f3 statistics tutorial or ppt
... Hi all, I am looking for a tutorial about f3 and f4 tests - with pictures :-). Do you know any ? best Christian ...
popul population genetics written 10 months ago by Genotepes940
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Simulating populations with coalescent model
... Hi, is anybody aware of a short beginner's tutorial for coalescent and using ms (and related software) for population simulation ? Thanks ...
coalescent snp ms written 15 months ago by Genotepes940 • updated 15 months ago by grant.hovhannisyan1.5k
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Material for calling in NGS - statistical view
... Hi all, I am preparing a short course on statistical tests for exome analysis (association in NGS) and I'd like to discuss a bit the statistical aspects of the calling - not the pipe-line - and integration of uncertainty in the downstream analyses. I have already some slides with the "Bayesian Cal ...
next-gen course snp written 3.3 years ago by Genotepes940 • updated 3.2 years ago by ivivek_ngs4.8k
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Comment: C: Genomic Correction
... Usually papers by Bacanu and Devlin are good (advanced) introductions to this : http://www.ncbi.nlm.nih.gov.gate2.inist.fr/pubmed/11754464 http://www.ncbi.nlm.nih.gov.gate2.inist.fr/pubmed/15514657 ...
written 6.5 years ago by Genotepes940
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Answer: A: Genomic Correction
... Hi basically you are correction for an inflation of your test statistic (here in Genome wide association studies). If you assume that most of your SNPs are NOT assciated with the trait of interest, then the overwhelming majority of statistical tests'p-values (one per SNP) should follow a uniform d ...
written 6.5 years ago by Genotepes940
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Number Of Snps By Maf
... I could not find a Table that explicitely estimates the number of SNPs by MAF bins in Human Genome (for European descent individuls). Obviously it is difficult becuase frequency is related to a population, the 1000 genomes combined low-pass whole genome and deep exome sequencing. I nthe 1000 G paper ...
maf snp written 6.5 years ago by Genotepes940
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Comment: C: Simulate Associated Phenotype From Existing Genotype Data In R
... So, does this mean you need to generate a model where imputed SNPs are causal? I think you'll need to put a threshold and give a plain genotype As for model generation, you are right. ...
written 6.6 years ago by Genotepes940
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Answer: A: How To Get Info On "Clinically Associated Snps"
... Maybe this means that theyr are associated in GWAs context (although I have no clue of why it is "clinical" as there are a lot of traits). Have a look at the updated list at NHGRI URL. http://www.genome.gov/gwastudies/#download and try your SNP on the browser. You may alos download the whole cata ...
written 6.6 years ago by Genotepes940

Latest awards to Genotepes

Popular Question 15 months ago, created a question with more than 1,000 views. For Getting Intensities For Genotype Calling In Axiom Cel Files With Apt
Popular Question 15 months ago, created a question with more than 1,000 views. For Positioning A Set Of ~20 Bases Dna Sequences
Popular Question 15 months ago, created a question with more than 1,000 views. For Getting Go-Annotation Data In Computer Readable Format
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Getting Intensities For Genotype Calling In Axiom Cel Files With Apt
Guru 3.2 years ago, received more than 100 upvotes.
Appreciated 6.2 years ago, created a post with more than 5 votes. For A: What Is Background Ld?
Appreciated 6.2 years ago, created a post with more than 5 votes. For A: Genotype Imputation And Population Substructure
Appreciated 6.2 years ago, created a post with more than 5 votes. For A: Strand-Orientation In Meta-Analysis With Plink
Appreciated 6.2 years ago, created a post with more than 5 votes. For A: What Are Phased And Unphased Genotypes?
Good Answer 6.2 years ago, created an answer that was upvoted at least 5 times. For A: What Is Background Ld?
Good Answer 6.2 years ago, created an answer that was upvoted at least 5 times. For A: Genotype Imputation And Population Substructure
Good Answer 6.2 years ago, created an answer that was upvoted at least 5 times. For A: What Are Phased And Unphased Genotypes?
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Getting Intensities For Genotype Calling In Axiom Cel Files With Apt
Popular Question 6.2 years ago, created a question with more than 1,000 views. For Getting Go-Annotation Data In Computer Readable Format
Supporter 6.2 years ago, voted at least 25 times.
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Genomic Correction
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Control For Population Stratification In Exome Sequencing Data
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: What Is Background Ld?
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: What Kind Of Bioinformatics Tutorials Would You Like To See Online?
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Any Recommendation On Program That Could Simulate Gwa Case/Control Data ?
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Using Kurtosis To Assess Significance Of Components From Independent Component A
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Genotype Imputation And Population Substructure
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Strand-Orientation In Meta-Analysis With Plink
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: Find The Extent Of A Peak In A Manhattan Plot
Teacher 6.2 years ago, created an answer with at least 3 up-votes. For A: What Are Phased And Unphased Genotypes?

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