User: Paul Shannon

gravatar for Paul Shannon
Paul Shannon750
Reputation:
750
Status:
Trusted
Location:
Last seen:
5 years, 8 months ago
Joined:
7 years, 7 months ago
Email:
p*******@fhcrc.org

Posts by Paul Shannon

<prev • 73 results • page 1 of 8 • next >
0
votes
1
answer
485
views
1
answers
Answer: A: active subnetwork determination
... Hi Benjamin, The BioNet package http://www.bioconductor.org/packages/release/bioc/html/BioNet.html is somewhat related to Ideker's approach. It uses expression data and reference networks (protein-protein interactions, primarily) to locate functional modules. There are a few other candidates ...
written 5.7 years ago by Paul Shannon750
0
votes
1
answer
728
views
1
answers
Comment: C: biogrid cytoscape plugin
... Hi Helen, May I ask what you are trying to do with the BioGrid plugin? All BioGrid interactions are avaialable programmatically with the new Bioc PSICQUIC package. Please describe (in some detail) what your goal is; we could then figure out if PSCICQUIC + RCytoscape will help. - Paul On Feb 3 ...
written 5.7 years ago by Paul Shannon750
0
votes
0
answers
487
views
0
answers
tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small
... Hi Coni, Inasmuch as things like this usually have a deterministic cause :} -- maybe you could check the free memory in your computer when the error message appears. Perhaps it is caused by an absence of free memory, a phenomenon which ought not to make a difference in anything but speed, but whi ...
network written 5.8 years ago by Paul Shannon750
0
votes
0
answers
573
views
0
answers
RCytoscape: tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small
... Hi Coni, This error, "tudelft.CytoscapeRPC.CytoscapeRPCCallHandler: width is too small" is mysterious. I saw a rash of them a few months ago, but never before, and never since. What version of Java are you running? My only suggestion is a weak one: to restart Cytoscape. Which maybe you have al ...
systemsbiology network rcytoscape written 5.8 years ago by Paul Shannon750
0
votes
1
answer
581
views
1
answer
bug in graph::addNode() w/ graph::edgeData()
... Hi Robert, The graphBAM addNode bug is now finally fixed. Thanks for your patience. The fix is available now in devel as graph 1.41.2. By mid-day Saturday, it will be available in release as graph 1.40.1. Thanks again for the excellent bug report. - Paul On Nov 7, 2013, at 7:04 AM, Robert C ...
graph written 5.8 years ago by Paul Shannon750 • updated 5.8 years ago by Robert Castelo2.3k
0
votes
1
answer
945
views
1
answers
Answer: A: How to compare GO term lists and create matching network?
... Hi Bernardo, As you suggest, you have a lot of options. Venn diagrams can be useful for a quick survey of overlapping group memberships, especially if (as in your case) you have no more than three groups. Google "R cran venn" and you will see a few. Your choice of technique should be guided by t ...
written 5.9 years ago by Paul Shannon750
0
votes
1
answer
620
views
1
answers
Answer: A: bug in graph::addNode() w/ graph::edgeData()
... Hi Robert, Thanks for the graphBAM bug report -- delivered, as always, in a truly helpful and reproducible manner, and with a proposed fix!. I will look into this and see if I have anything to add. If you have a moment, and have not already given it a try, you could test out your fix by running ...
written 6.0 years ago by Paul Shannon750
0
votes
1
answer
1.6k
views
1
answers
Comment: C: Directed MST (Edmond's Algorithm)
... On Oct 22, 2013, at 9:39 AM, Vincent Carey wrote: > Do we need some investment in interoperability with igraph? Maybe this is old news, or falls short of the mark, but two functions from igraph provide some interoperability: igraph.from.graphNEL(graphNEL, name = TRUE, weight = TRUE, ...
written 6.0 years ago by Paul Shannon750
0
votes
1
answer
2.3k
views
1
answer
getting a list of genomic sequences from a list of gene names
... To summarize our off-list discussion, and present our final suggested answer, using a sample entrez geneID to demonstrate, we offer the code shown below. A somewhat lengthy exposition of the 9 steps involved will be found below, following the 18 lines of excutable code. Thanks for posing this ques ...
written 6.3 years ago by Paul Shannon750 • updated 6.3 years ago by Michael Lawrence11k
1
vote
1
answer
743
views
1
answer
copy number segment calling with cn.mop when just one sample?
... Hi Gunter, It appears that cn.mops has no mode for calling copy number segments when just one sample is present. Am I interpreting the documentation properly? Thanks for the fine package! - Paul ...
cn.mops written 6.4 years ago by Paul Shannon750 • updated 4.3 years ago by Günter Klambauer540

Latest awards to Paul Shannon

Popular Question 5.7 years ago, created a question with more than 1,000 views. For Motif search -- access to JASPAR, MotIV package, more TF-PWM relationships?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For QuasR: how to use an indexed reference genome?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For Motif search -- access to JASPAR, MotIV package, more TF-PWM relationships?
Popular Question 5.7 years ago, created a question with more than 1,000 views. For getting a list of genomic sequences from a list of gene names
Popular Question 5.7 years ago, created a question with more than 1,000 views. For getting a list of genomic sequences from a list of gene names

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 408 users visited in the last hour