User: Paul Shannon

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Paul Shannon360
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Posts by Paul Shannon

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use MotifDb package with rGADEM?
... Reading through the rGADEM man pages, I have yet to figure out how to supply PWMs of my own choosing for rGADEM to match against.  MotifDb provides a method ("query") for extracting a list of matrices by various criteria, for instance: as.list(query(MotifDb, "MA0079.3"))[[1]]            1        ...
matchpwm written 15 days ago by Paul Shannon360
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Answer: A: total number of unique transcription factors in MotifDB
... Hi Scott, As a preface to my answer: we have added three new methods to the new release of MotifDb: geneToMotif motifToGene associateTranscriptionFactors All three require a "source" argument, either "MotifDb" or "TFClass" - thus offering two data sources for the sometimes imprecise business ...
written 7 months ago by Paul Shannon360
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Answer: A: PSICQUIC - Provide own local database of interactions
... Hi Alaa, You may find the Bioconductor RefNet package fits your needs.  It is a wrapper around PSICQUIC and it provides a straightforward method for adding your own interactions.   Inspired by PSICQUIC, RefNet defines a data.frame format. These interactions have been expressed in the standard RefN ...
written 8 months ago by Paul Shannon360
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Answer: A: How to make a MotifDb object from pwm/pfm files?
... Yiwei, The process is described in the programmer's guide:     https://github.com/Bioconductor-mirror/MotifDb/blob/master/vignettes/programmersGuide.txt The (sometimes) hard part of adding new matrices is obtaining  metadata for each new matrix, and transforming it into the DataTable.  We would b ...
written 8 months ago by Paul Shannon360
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Answer: A: Fail to load "MotifDb" package
... Pengcheng Yang, Sorry you encountered trouble with MotifDb.   The same error, with a solution proposed, is reported here:  https://support.bioconductor.org/p/93695/ Could you give that a try?  - Paul   ...
written 14 months ago by Paul Shannon360
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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 14 months ago by Paul Shannon360 • updated 14 months ago by Valerie Obenchain ♦♦ 6.5k
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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 23 months ago by Paul Shannon360
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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 23 months ago by Paul Shannon360
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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 23 months ago by Paul Shannon360
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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 23 months ago by Paul Shannon360

Latest awards to Paul Shannon

Scholar 14 months ago, created an answer that has been accepted. For A: taking intersection between 6 networks by graph.intersect
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Fail to load "MotifDb" package
Scholar 2.2 years ago, created an answer that has been accepted. For A: taking intersection between 6 networks by graph.intersect

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