User: Paul Evans

gravatar for Paul Evans
Paul Evans180
Reputation:
180
Status:
Trusted
Location:
Last seen:
9 years, 10 months ago
Joined:
11 years, 8 months ago
Email:
p********@yahoo.com

Posts by Paul Evans

<prev • 18 results • page 1 of 2 • next >
0
votes
2
answers
887
views
2
answers
Comment: C: dbSNP - getting details of Pubmed ID for a SNP
... Thanks Sean. Yes, I'd like to do it for a large set of snp ids. thanks! ________________________________ From: Sean Davis Cc: Bioconductor@stat.math.ethz.ch Sent: Sat, January 9, 2010 8:48:05 PM Subject: Re: [BioC] dbSNP - getting details of Pubmed ID for a SNP > Hi, > > I had a set ...
written 9.9 years ago by Paul Evans180
0
votes
2
answers
887
views
2
answers
dbSNP - getting details of Pubmed ID for a SNP
... Hi, I had a set of snp ids (e.g. 'rs11805303'). Is there any package that will let me access dbSNP database and return the Pubmed IDs of articles that have cited that particular snp id. For example, for 'rs11805303', it will return Pubmed IDs: 17554300,18533027,19522770 thanks! [[altern ...
snp written 9.9 years ago by Paul Evans180 • updated 20 months ago by hsiaoyi05040
0
votes
0
answers
499
views
0
answers
SNP/GWAS - snp id to Pubmed ID through dbSNP
... Hi, Ihad a set of snp ids (e.g. 'rs11805303'). Is there any package that will let me access dbSNP database and return the Pubmed IDs of articles that have cited that particular snp id. For example, for 'rs11805303', it will return Pubmed IDs: 17554300,18533027,19522770 thanks! [[alternat ...
snp written 9.9 years ago by Paul Evans180
0
votes
2
answers
957
views
2
answers
exon and transcription start site locations
... Hi, I wanted to find out the exact locations on the genes (and the chromosome) for exons and transcription start sites in the human genome. Is there any package that will let me get at this information? Alternatively, how should I go about getting this information? thanks! [[alternative ...
transcription go written 10.0 years ago by Paul Evans180 • updated 10.0 years ago by Michael Lawrence620
0
votes
1
answer
826
views
1
answer
Plot SNP -log10 pvalues vs chromosomal position
... Hi, I wanted to plot the -log10 p-values of SNPs vs their chromosomal positions. I have an input file which looks like: Chr Ref Position p-value 1 rs100045 456789 0.00005 3 rs12345 23456 0.00004 . . . Which bioconductor package would be best for this? I looked at GenABEL and snp.plotter, but both o ...
snp written 10.1 years ago by Paul Evans180 • updated 10.1 years ago by Vincent J. Carey, Jr.6.3k
0
votes
0
answers
604
views
0
answers
PFAM analysis packages?
... Hi, Are there any packages that will aid in the analysis of genes related to a particular PFAM family? For example, the GOstats, KEGGSOAP package help in analysis (e.g. visualizing where individual genes may be mapped in the pathway) of genes w.r.t. pathways. Are there any similar packages availabl ...
pathways gostats written 10.6 years ago by Paul Evans180
0
votes
1
answer
655
views
1
answer
GOstats: HyperGTest for KEGG
... Hi, I was trying to get significant KEGG terms for yeast. Previously, I used the "YEAST" package, but I am now shifting to the "org.Sc.sgd.db" package. A sample of the code, and the error I get is reproduced below: ------------------------------------------------ Begin code ----------------------- ...
annotation go yeast hgu133a hgu133b hgu133plus2 hgu95a hgu95av2 hgug4110b hgug4112a written 10.8 years ago by Paul Evans180 • updated 10.8 years ago by Marc Carlson7.2k
0
votes
0
answers
658
views
0
answers
GOstats: hyperGTest for KEGG with org.Sc.sgd.db
... Hi, I was trying to get significant KEGG terms for yeast. Previously, I used the "YEAST" package, but I am now shifting to the "org.Sc.sgd.db" package. A sample of the code, and the error I get is reproduced below: ------------------------------------------------ Begin code ----------------------- ...
0
votes
0
answers
379
views
0
answers
KEGGgraph ??
... Hi, I want to map some KEGG terms on the KEGG hierarchy. I have been looking at keggorth package to do this. Essentially, I would like to map two sets of KEGG pathways (with two different colors) onto the hierarchy. I have done this with GO terms using the GOgraph function in GOstats package. So, ...
pathways go gostats keggorth kegggraph written 11.1 years ago by Paul Evans180
0
votes
1
answer
590
views
1
answer
Protein structure analysis
... Hi, I have a set of genes and would like to conduct an analysis to see how much similarity (dis-similarity) there is between the surfaces/structures of the proteins they encode. Which packages should I be looking at? [[alternative HTML version deleted]] ...
written 11.1 years ago by Paul Evans180 • updated 11.1 years ago by Diego Diez750

Latest awards to Paul Evans

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour