User: pshannon
pshannon • 80
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Posts by pshannon
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... 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 3.6 years ago by
pshannon • 80
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... 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 3.9 years ago by
pshannon • 80
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... 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 3.9 years ago by
pshannon • 80
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... Thanks, Keith: good catch. I'll update the pmid in RefNet.
- Paul
...
written 4.0 years ago by
pshannon • 80
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... 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 4.0 years ago by
pshannon • 80
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... 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 4.0 years ago by
pshannon • 80
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... 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 4.0 years ago by
pshannon • 80
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1
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... 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 4.5 years ago by
pshannon • 80
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... 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 4.5 years ago by
pshannon • 80
1
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... 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 ...
written 4.5 years ago by
pshannon • 80
Latest awards to pshannon
Popular Question
3.5 years ago,
created a question with more than 1,000 views.
For Shiny app for RefNet, PSICQUIC: annotated protein/protein interactions
Teacher
4.0 years ago,
created an answer with at least 3 up-votes.
For A: Mapping genome regions to gene symbols
Scholar
4.0 years ago,
created an answer that has been accepted.
For A: Mapping genome regions to gene symbols
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