User: Vincent Laufer

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

<prev • 179 results • page 1 of 18 • next >
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Is there a database or catalog of the proteins secreted through the Type 3 Secretion System available?
... 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 ...
metagenomics microbiology written 3 months ago by Vincent Laufer1.1k
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Programmatically kicking off cellranger based on fastq folder format
... 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 ...
10x scrna-seq fastq cellranger written 5 months ago by Vincent Laufer1.1k
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Forum: What are the 10 most exciting developments on the horizon in precision medicine?
... 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 ...
precision medicine forum written 14 months ago by Vincent Laufer1.1k
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Go Partition Database or another like tool
... 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 ...
gene ontology hierarchy go dag written 17 months ago by Vincent Laufer1.1k
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Options for labeling pathways with higher-order ontologies
... 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" ...
pathways gene ontology kegg go biocarta written 17 months ago by Vincent Laufer1.1k
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Comment: C: Selection of a "suggestive" level of association in a GWAS study
... Thank you for clarifying, lindsay! ...
written 17 months ago by Vincent Laufer1.1k
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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 18 months ago by Vincent Laufer1.1k
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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 19 months ago by Vincent Laufer1.1k
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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 19 months ago by Vincent Laufer1.1k
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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 2.3 years ago by Vincent Laufer1.1k

Latest awards to Vincent Laufer

Popular Question 12 months ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Convert .csv to .vcf
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: hypergeometric distribution for proximal gene enrichment
Popular Question 17 months ago, created a question with more than 1,000 views. For Finding public ChIP-seq data for various tissue types
Appreciated 18 months ago, created a post with more than 5 votes. For A: hypergeometric distribution for proximal gene enrichment
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Finding public ChIP-seq data for various tissue types
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Most common method for looking at LD independent SNPs
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Odds Ratio Confidence Intervals in SNP Test
Popular Question 2.2 years 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 2.2 years ago, created an answer that has been accepted. For A: Delete Text between two strings sed, awk
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: Hardy-Weinberg assumptions in variant calling

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