User: pshannon

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pshannon80
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Posts by pshannon

<prev • 15 results • page 1 of 2 • next >
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Answer: A: Identifying TF binding sites (Motifdb + TxDb.Hsapiens.UCSC.hg19.knownGene)
... Hi LIsa, This is a very well-posed question!   Thank you.    I contributed the MotifDb package a couple of years ago, but I am not intimate with the details of TF binding sites and their distribution.  However, I notice that the JASPAR-CORE pwm for Myc is just 12 bases wide but TP53 is 20.  In my ...
written 2.1 years ago by pshannon80
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Answer: A: RCytoscape: unable to find an inherited method for function ‘nodeData<-’
... The best course -- which we have discussed off-line, and which I believe seems promising to you -- is to switch to the new RCy3 package, currently submitted to Bioc, available on github, and for which we are actively soliciting testers. If you will send me some more information I will try to reprod ...
written 2.4 years ago by pshannon80
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Answer: A: How to find TF binding sites for particular TF's within +- 1000 bases of gene TS
... Hi Duncan, A good place to start (if you have not already done so) is to read through our Bioc workflow, "Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching".    http://bioconductor.org/help/workflows/generegulation/ As mentioned there -- but not yet demonstrate ...
written 2.5 years ago by pshannon80
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Answer: A: RefNet: source/data preparation used for Gerstein et al (2012) human TF data?
... Thanks, Keith: good catch.  I'll update the pmid in RefNet.   - Paul ...
written 2.5 years ago by pshannon80
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Answer: A: RefNet: source/data preparation used for Gerstein et al (2012) human TF data?
... Hi Keith, The RefNet gerstein-2012 data interactions are from   http://archive.gersteinlab.org/proj/Hierarchy_Rewiring/PNAS_hier/Hs_Tr.txt If other (and possibly more recent) interaction data sets are of compelling interest, let us know.  The 4 which are built in to RefNet now ('native'; they liv ...
written 2.5 years ago by pshannon80
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Answer: A: PSICQUIC addGeneInfo invalid attribute names
... Hi Anaïs, Biomart changed the name of this attribute to simply "uniprot_swissprot" about the first of the year.  We discovered this -- just as you did! -- and made the fix in PSICQUIC version 1.5.7. biocLite("PSICQUIC")   ought to solve the problem. - Paul ...
written 2.5 years ago by pshannon80
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Answer: A: Mapping genome regions to gene symbols
... Another approach uses Steffen Durink's fine biomaRt package, a  contribution to Bioconductor of many year's standing.  In its simplest form just two lines of code gets you all the genes in one copy number region: library(biomaRt) mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl ...
written 2.6 years ago by pshannon80
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Answer: A: ConnectionMap rankMatrix value
... Hi Y.L, The cmap data is from the Broad; we offer it with their permission.   I believe you can find the answer to your question in their help docs, which can be found here:   http://www.broadinstitute.org/cmap/help_topics_linkified.jsp Let us know if that provides what you are looking for.   I c ...
written 3.0 years ago by pshannon80
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Answer: A: Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
... Hi Mark, Thanks for keeping at this.   You have an out-of-date copy of RefNet.  You need version 1.2.0.  Please try this in your R session: source("http://bioconductor.org/biocLite.R") biocLite("RefNet") suppressPackageStartupMessages(library(RefNet)) dir(system.file(package="RefNet", "apps") Y ...
written 3.1 years ago by pshannon80
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Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
... In addressing some problems reported with using the RefNet package last week, I promised to follow up with an account of the RefNet/PSICQUIC shiny app.   For background: the Bioc RefNet package  modestly extends the PSICQUIC package ("Proteomics Standards Initiative Query Interface").  Together the ...
network shiny interactions written 3.1 years ago by pshannon80

Latest awards to pshannon

Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Mapping genome regions to gene symbols
Scholar 2.5 years ago, created an answer that has been accepted. For A: Mapping genome regions to gene symbols

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