User: Vincent Laufer
Vincent Laufer • 1.1k
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Posts by Vincent Laufer
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... Id be interested in finding a database of all the proteins that are secreted through the T3SS across all organisms that possess one.
It might be possible to catalog them by species by hand, but I think to get as complete a list as can be gotten for each organism, might require an algorithmic approa ...
written 6 days ago by
Vincent Laufer • 1.1k
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... I am attempting to automate a scRNA-seq workflow for 10x genomics data to be processed by cellranger.
As described in this link: [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input][1] , fastQ files are made in several ways, and the folder struct ...
written 7 weeks ago by
Vincent Laufer • 1.1k
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... Hi everyone,
I have just spent some time away, and I feel a bit out of the loop with respect to genomics and precision medicine at the moment.
I am writing to learn about any developments that have occurred in the last 12 months (or that you think will occur soon) in precision medicine, and how yo ...
written 10 months ago by
Vincent Laufer • 1.1k
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... Does the [Go Partition Database][1], or any like entity, still exist on the web?
To clarify, I want to group pathways together into higher-level super pathways or ontologies. Specifically, I would like to do more than group the pathways based on information content; if at all possible I would like ...
written 13 months ago by
Vincent Laufer • 1.1k
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... I have some RNA sequencing data on which I have run several pathway analyses.
I've noticed that the pathways for my wild type animals relate more strongly to cell cycling, and less strongly to immune response. By contrast, the differentially regulated pathways for my KO animals are heavily "immune" ...
written 13 months ago by
Vincent Laufer • 1.1k
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... Thank you for clarifying, lindsay! ...
written 13 months ago by
Vincent Laufer • 1.1k
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... 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 14 months ago by
Vincent Laufer • 1.1k
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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 16 months ago by
Vincent Laufer • 1.1k
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... Do you have the pathways annotated?
In what ways do you want to compare them? ...
written 16 months ago by
Vincent Laufer • 1.1k
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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 2.0 years ago by
Vincent Laufer • 1.1k
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