User: Paul Shannon

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Paul Shannon360
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Posts by Paul Shannon

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Comment: C: BiocParallel: database disk image is malformed
... Thanks, Martin.   Funny thing, all these years in and I did not know that the org db files were in-memory sqlite databases - with not only implicit connect and disconnect, but explicit versions also.  Seeing that in your example I will now code appropriately. ...
written 3 months ago by Paul Shannon360
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Comment: C: BiocParallel: database disk image is malformed
... Hi Martin, Thanks for your offer.  Here is a minimal example:  9 lines, a few of which are just for set up.    In brief: read-only access via select to org.Hs.eg.db, with larg-ish query keys, frequently (but not always) produces the error, when more than two workers are requested:  database disk ...
written 3 months ago by Paul Shannon360
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Comment: C: BiocParallel: database disk image is malformed
... Thank you, Martin.  The ipclock is an elegant solution - but might not be needed after all.   Here is an example where, with atomic dbConnect, dbGetQuery and dbDisconnect, any number of workers can query the database without conflict.  library(BiocParallel) library(RPostgreSQL) dbcall <- functi ...
written 3 months ago by Paul Shannon360
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BiocParallel: database disk image is malformed
... We run an involved process, repeatedly for different genes, using BiocParallel.  With SerialParams or MultiCorpParam(workers=2), the jobs - no matter how many - run to completion.   With workers > 2, we see consistent failure with the rather cryptic error message     "database disk image is malf ...
biocparallel databases written 3 months ago by Paul Shannon360 • updated 3 months ago by Martin Morgan ♦♦ 22k
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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 5 months 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 12 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 13 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 13 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 19 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 19 months ago by Paul Shannon360 • updated 19 months ago by Valerie Obenchain ♦♦ 6.6k

Latest awards to Paul Shannon

Scholar 19 months ago, created an answer that has been accepted. For A: taking intersection between 6 networks by graph.intersect
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Fail to load "MotifDb" package
Scholar 2.6 years ago, created an answer that has been accepted. For A: taking intersection between 6 networks by graph.intersect

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