User: Vincent Laufer

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Vincent Laufer1.0k
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Posts by Vincent Laufer

<prev • 173 results • page 1 of 18 • next >
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Comment: C: Selection of a "suggestive" level of association in a GWAS study
... this is interesting - of course the bulk of the literature of which I am aware derives an understanding of these levels from the number of effectively independent markers. so would be odd to use a pig based threshold unless they have similar levels of LD and numbers of haploblocks ...
written 15 days ago by Vincent Laufer1.0k
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Comment: C: GWAS, quantitative traits
... perhaps my answer to this post can help you https://www.biostars.org/p/176238 ...
written 9 weeks ago by Vincent Laufer1.0k
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Comment: C: Comparing the metabolic pathways of pathogen and host using KEGG?
... Do you have the pathways annotated? In what ways do you want to compare them? ...
written 10 weeks ago by Vincent Laufer1.0k
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Answer: A: Should I include multi-mapped reads for analysis that does not require significa
... @k.woolf - *Because your goals still rely on quantitative comparisons,* I would recommend you use either unique reads only, or that you use a published method of partial transcript estimation. To explore this, let's think about two simple approaches, and try to identify problems. Consider a singl ...
written 10 months ago by Vincent Laufer1.0k
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Comment: C: Turning a Reference Genome Into a File With Single Nucleotide Positions (Essenti
... Hey, I think I understand, but could you elaborate on the format of the referenced genome file? ...
written 10 months ago by Vincent Laufer1.0k
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Comment: C: hands on resources for high school students with advanced CS skills
... not at all. i will remember this for the future. thanks. ...
written 10 months ago by Vincent Laufer1.0k
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Forum: hands on resources for high school students with advanced CS skills
... Hi all, I was hoping to crowdsource ideas to help get a high school student started thinking about biology and informatics. The student I have in mind is a gifted computer programmer, my understanding is he can already work on games requiring 3D modeling, etc. His knowledge of math and biology do ...
forum informatics education high school written 10 months ago by Vincent Laufer1.0k • updated 10 months ago by h.mon25k
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Comment: C: How to perform differential gene expression analysis between two closely related
... Although this does not address your initial question, I wanted to propose a downstream QC step that can help you decide if the approach you do use was successful or not. After finding a mapping that is acceptable (for example the 2-step assembly per ecotype approach recommended by @genomemax in his ...
written 10 months ago by Vincent Laufer1.0k
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Comment: C: Convert (Copy Number Variation) CNV to gene
... I agree with the comment above; i.e. we need to know what exactly you mean. Is what you want to say "how can I map the location of each CNV to one or more genes, provided they overlap?" Second, I would like to ask *what kind of data you have* (e.g. whole genome sequencing / microarray / multiple / ...
written 10 months ago by Vincent Laufer1.0k
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Function returning % trait explained for a SNP given effect size, MAF, prevalence, etc. for a complex trait
... Hello all, Is there a function written in R or another language of the form: Variance_Explained <- get_var_exp(effect_size, minor_allele_frequency, [other args]) Specifically, on page 25 of the supplemental methods of Stahl et al. 2012 (see https://www.nature.com/articles/ng.2232 ), an eq ...
R genetic variance explained risk score written 11 months ago by Vincent Laufer1.0k • updated 10 months ago by zx87547.5k

Latest awards to Vincent Laufer

Appreciated 5 weeks ago, created a post with more than 5 votes. For A: hypergeometric distribution for proximal gene enrichment
Popular Question 8 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Popular Question 8 months ago, created a question with more than 1,000 views. For Finding public ChIP-seq data for various tissue types
Popular Question 8 months ago, created a question with more than 1,000 views. For Most common method for looking at LD independent SNPs
Popular Question 8 months ago, created a question with more than 1,000 views. For Locus Zoom Issuing "No valid markers in VCF file" on a VCF created in Plink 1.9
Scholar 8 months ago, created an answer that has been accepted. For A: Delete Text between two strings sed, awk
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling
Guru 13 months ago, received more than 100 upvotes.
Popular Question 13 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Popular Question 14 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: hypergeometric distribution for proximal gene enrichment

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