User: Vincent Laufer

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Vincent Laufer1000
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Posts by Vincent Laufer

<prev • 170 results • page 1 of 17 • next >
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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 3 months ago by Vincent Laufer1000
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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 3 months ago by Vincent Laufer1000
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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 3 months ago by Vincent Laufer1000
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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 3 months ago by Vincent Laufer1000 • updated 3 months ago by h.mon21k
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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 3 months ago by Vincent Laufer1000
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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 3 months ago by Vincent Laufer1000
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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 4 months ago by Vincent Laufer1000 • updated 3 months ago by zx87545.6k
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Comment: C: Co-occuring mutations analysis
... this question could mean almost anything. any software program including a function or two dealing with linkage disequilbrium technically meets this definition. do you have a more specific question? perhaps relating to a given field such as cancer biology? ...
written 7 months ago by Vincent Laufer1000
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Comment: C: High-quality visualization of GSEA data illustrating relationships between multi
... yes i can do this, however it does not address the questions as posted above. ...
written 8 months ago by Vincent Laufer1000
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High-quality visualization of GSEA data illustrating relationships between multiple pathways.
... I am finishing up a collaboration for a group for whom I have been analyzing some RNA sequencing data. I have already generated the "standard" figures for GSEA analysis, (e.g. barcode plots, leading edge heatmaps, a joyplot, and a few other things that visualize **individual pathways.**). What I ...
figure gsea written 8 months ago by Vincent Laufer1000

Latest awards to Vincent Laufer

Popular Question 7 weeks 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 7 weeks ago, created an answer that has been accepted. For A: Delete Text between two strings sed, awk
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling
Popular Question 6 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Guru 6 months ago, received more than 100 upvotes.
Popular Question 7 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: hypergeometric distribution for proximal gene enrichment
Scholar 18 months ago, created an answer that has been accepted. For A: Delete Text between two strings sed, awk
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling
Popular Question 19 months ago, created a question with more than 1,000 views. For Selection of a "suggestive" level of association in a GWAS study
Popular Question 21 months ago, created a question with more than 1,000 views. For List of causal variants for autoimmune diseases
Voter 21 months ago, voted more than 100 times.

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