User: areyoujokingme

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New User
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United States
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1 year, 7 months ago
Joined:
3 years, 1 month ago
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Posts by areyoujokingme

<prev • 24 results • page 1 of 3 • next >
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Querying MetaboAnalyst Dynamically for Multiple Requests - API?
... I want to query MetaboAnalyst's Pathway analysis tool for many, many metabolite sets. I can't possibly do this manually, one metabolite set at a time. Is there a way to query MetaboAnalyst, via an API, or any other clever way to submit multiple jobs? ...
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Querying KEGG RDF graph Comparing to WikiPathways RDF "schema"
... I want to get all interactions between Metabolites and Gene Products in the KEGG database. I've done this before querying WikiPathways with the below SPARQL query. I can't seem to "break into" KEGG's SPARQL "schema" to translate this query in such a way that probes KEGG for the same information. * ...
rdf semantic web wikipathways sparql kegg written 21 months ago by areyoujokingme60
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Comment: C: Haploview CG limit error?
... Unfortunately, no. :( ...
written 21 months ago by areyoujokingme60
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Extract Graph Structure from WikiPathways into R igraph?
... I am tasked with the job of porting WikiPathways into an igraph object in R. I'm new to WikiPathways, and know about rWikiPathways R package, and have downloaded the .txt files of all human pathways. I am also decently new to SPARQL, though it's reminiscent of SQL imho. Basically, how would I go ...
R wikipathways igraph written 23 months ago by areyoujokingme60
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Answer: A: Get Parent GO Term for all GO Terms in a Vector?
... It turns out if you set the font.size in the graphNEL object, you can see the node names in the plot of the inducedTermGraph. Setting font.size to >20 worked for me! ...
written 2.1 years ago by areyoujokingme60
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Get Parent GO Term for all GO Terms in a Vector?
... I have a vector of GOIDs that are specific GO IDs outputted from an enrichment analysis. I want to cluster my GOIDs by their parent GOID term. I used GOstats to do my enrichment analysis, and I have noticed there is an inducedTermGraph, which outputs a graphNEL object of direct children and directio ...
parent dag go ontology written 2.1 years ago by areyoujokingme60
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Comment: C: Using VCFTools (v0.1.13) with ExAC (release 0.3.1)
... Thanks for writing an issue! Hopefully we hear from them soon! ...
written 2.2 years ago by areyoujokingme60
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Comment: C: Using VCFTools (v0.1.13) with ExAC (release 0.3.1)
... I just found the version number of ExAC, and it is actually v4.2! This cannot be a version issue, now. Can you explain how it's possible for ExAC to have a bug? For example, why did you paste the line above? Sorry if I'm missing something obvious! ...
written 2.2 years ago by areyoujokingme60
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Using VCFTools (v0.1.13) with ExAC (release 0.3.1)
... I'm trying to extract allele frequency information for all variants in the latest ExAC data release. I'm currently using vcftools version 0.1.13, and am coming into errors that relate, I *think*, to versions. When I validate the ExAC data VCF file, I get an error message for every INFO line in the ...
format exac vcftools written 2.2 years ago by areyoujokingme60 • updated 2.2 years ago by Pierre Lindenbaum107k
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RnBeads and beta-value matrix data format
... I'm not super familiar with different data formats for methylation data, but I have a raw data matrix with the beta values (B = methylation signal / (methylation signal + unmethylated signal)) in matrix form, where the rows are the CpG loci IDs (Illumina 450K is the platform) and the columns are the ...
R methylation infinium450k rnbeads written 2.5 years ago by areyoujokingme60 • updated 2.3 years ago by Biostar ♦♦ 20

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Scholar 2.1 years ago, created an answer that has been accepted. For A: Get Parent GO Term for all GO Terms in a Vector?

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