User: Vincent Laufer
Vincent Laufer • 1000
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Posts by Vincent Laufer
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... @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 Laufer • 1000
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... Hey,
I think I understand, but could you elaborate on the format of the referenced genome file? ...
written 3 months ago by
Vincent Laufer • 1000
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... not at all. i will remember this for the future. thanks. ...
written 3 months ago by
Vincent Laufer • 1000
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... 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 ...
written 3 months ago by
Vincent Laufer • 1000
• updated
3 months ago by
h.mon ♦ 21k
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... 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 Laufer • 1000
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... 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 Laufer • 1000
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... 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 ...
written 4 months ago by
Vincent Laufer • 1000
• updated
3 months ago by
zx8754 ♦ 5.6k
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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 Laufer • 1000
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... yes i can do this, however it does not address the questions as posted above. ...
written 8 months ago by
Vincent Laufer • 1000
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...
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 ...
written 8 months ago by
Vincent Laufer • 1000
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