User: Paul Shannon

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Paul Shannon370
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Posts by Paul Shannon

<prev • 42 results • page 2 of 5 • next >
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3.5 release schedule?
... https://bioconductor.org/developers/release-schedule/  appears to be last fall’s schedule, for 3.4.  Is the 3.5 schedule available? Thanks!  - Paul  ...
bioconductor written 2.1 years ago by Paul Shannon370 • updated 2.1 years ago by Valerie Obenchain6.7k
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Answer: A: interactive networks from WGCNA clusters
... Hi Chris, Have you tried using one of the cytoscape.js native layouts?  For instance:   layout(rcy, "cose") Where rcy is an RCyjsClass object   There are a handful of cyjs layout strategies. layoutStrategies(rcy) will show you the full list.  cose is a "Compound Spring Embedder" and m ...
written 2.8 years ago by Paul Shannon370
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Comment: C: WGCNA network visualisation in RCyjs
... In my code you will see   diag(m.cor) <- 0 This removes the self edges implied by the correlation matrix.  Make that change before you create the graph. ...
written 2.8 years ago by Paul Shannon370
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Answer: A: WGCNA network visualisation in RCyjs
... Christopher, Sorry for my delay.   Here is a complete example modeled after yours.  Not having access to your E.rna matrix, I generated a small random network library(RCyjs) set.seed(3) size <- 5 m <- matrix(runif(size * size), nrow=size, dimnames=list(LETTERS[1:size], LETTERS[1:size])) m.c ...
written 2.8 years ago by Paul Shannon370
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Answer: A: WGCNA network visualisation in RCyjs
... Hi Christopher, As you say, RCyjs (and RCy3) expect graphNEL objects, which are defined in the Bioconductor graph package. It is quite easy  to convert among the various common graph/network representations.  If you will provide a small reproducible example (a few lines of code ought to be enough) ...
written 2.9 years ago by Paul Shannon370
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Answer: A: taking intersection between 6 networks by graph.intersect
... Angel, I'd be glad to help.  Can you provide a small, focused and reproducible example?     - Paul ...
written 2.9 years ago by Paul Shannon370
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Answer: A: Problem with biomart's listMarts function
... biomaRt is now broken for me also.   Following Johannes suggestion: readLines("http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL") Error in file(con, "r") : cannot open the connection In addition: Warning message: In file(con, "r") : too many re ...
written 3.0 years ago by Paul Shannon370
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Comment: C: filterVcf by sample id
... Thanks, Val.  An elegant solution, just what I needed.   ...
written 3.1 years ago by Paul Shannon370
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Comment: C: filterVcf by sample id
... Just what I was looking for.   Thanks, Julian! ...
written 3.1 years ago by Paul Shannon370
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filterVcf by sample id
... I have some very large Alzheimer’s Disease vcf files, one per chromosome, 808 samples (affected and unaffected patients) in each. We can stratify those samples by their phenotype.  I want to filter the vcf so that,for example, there are only 25 advanced AD samples (columns)  in the GT matrix,  and ...
variantannotation written 3.1 years ago by Paul Shannon370 • updated 3.1 years ago by Valerie Obenchain6.7k

Latest awards to Paul Shannon

Scholar 2.1 years ago, created an answer that has been accepted. For A: taking intersection between 6 networks by graph.intersect
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Fail to load "MotifDb" package
Scholar 3.1 years ago, created an answer that has been accepted. For A: taking intersection between 6 networks by graph.intersect

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