User: Vincent Laufer

gravatar for Vincent Laufer
Vincent Laufer1.1k
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Posts by Vincent Laufer

<prev • 176 results • page 2 of 18 • next >
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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 11 months ago by Vincent Laufer1.1k
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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 11 months ago by Vincent Laufer1.1k
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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 12 months ago by Vincent Laufer1.1k • updated 11 months ago by zx87547.7k
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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 15 months ago by Vincent Laufer1.1k
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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 16 months ago by Vincent Laufer1.1k
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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 16 months ago by Vincent Laufer1.1k
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Comment: C: Deseq2 question of a single factor with 3 levels
... It may be time to consider this. Although I agree that *most* people who crosspost without explicitly saying it is a crosspost necessitate unnecessary work for the community, it is also the case the crossposting can help internet communities provided that those queries are linked. Therefore althou ...
written 17 months ago by Vincent Laufer1.1k
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Comment: C: Deseq2 question of a single factor with 3 levels
... Does this website have a formal policy on etiquette for crossposting? ...
written 17 months ago by Vincent Laufer1.1k
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Comment: C: How to keep a log of columns removed from edited MSA?
... Please provide a sample of one of the input MSA files and the desired output file. ...
written 18 months ago by Vincent Laufer1.1k
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Comment: C: Conditioning association summary statistics using a correlation matrix.
... @Jean-Karim - Thank you for your post. I will reflect on this. I will conduct a search on my own. However, if you have any manuscripts or even textbooks in mind, I will be sure to take a look at those too. ...
written 19 months ago by Vincent Laufer1.1k

Latest awards to Vincent Laufer

Popular Question 13 days ago, created a question with more than 1,000 views. For Finding public ChIP-seq data for various tissue types
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: hypergeometric distribution for proximal gene enrichment
Popular Question 9 months ago, created a question with more than 1,000 views. For Most common method for looking at LD independent SNPs
Popular Question 9 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Popular Question 9 months ago, created a question with more than 1,000 views. For Finding public ChIP-seq data for various tissue types
Popular Question 9 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 9 months ago, created an answer that has been accepted. For A: Delete Text between two strings sed, awk
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling
Guru 14 months ago, received more than 100 upvotes.
Popular Question 14 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Popular Question 15 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test

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