User: Paul Shannon

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Paul Shannon370
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Posts by Paul Shannon

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DeepBlueR - query all annotations across region
... Just taking my first look at DeepBlueR, read the man pages and the vignette, ran through some of the examples. Good stuff here - but I am a little confused about formulating my typical queries. For example, in naive pseudo-code, to obtain all the ChIP-seq hits in a small region of the hg38 genome: ...
chip-seq queries written 13 days ago by Paul Shannon370 • updated 12 days ago by Bioconductor Community ♦♦ 0
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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 6 months ago by Paul Shannon370
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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 6 months ago by Paul Shannon370
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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 6 months ago by Paul Shannon370
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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 6 months ago by Paul Shannon370 • updated 6 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 8 months ago by Paul Shannon370
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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 15 months ago by Paul Shannon370
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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 16 months ago by Paul Shannon370
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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 16 months ago by Paul Shannon370
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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 22 months ago by Paul Shannon370

Latest awards to Paul Shannon

Scholar 22 months ago, created an answer that has been accepted. For A: taking intersection between 6 networks by graph.intersect
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Fail to load "MotifDb" package
Scholar 2.8 years ago, created an answer that has been accepted. For A: taking intersection between 6 networks by graph.intersect

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