Displaying 20 results from an estimated 345 matches for "enriching".
2012 Jul 21
1
GOstats: get genes for corresponding enriched GO term
Hi,
I used GOstats to perform enrichment test on a set of genes (20).
There are 7 GO terms with pvalue less than cuttoff and therefore shown in
the result table.
How can I get the information that which gene in the input gene set belong
to which GO term of these enriched GO terms?
Thanks for any comments.
best,
Tim
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2018 Mar 12
0
pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
Hello all,
I would like to introduce our group's new bioinformatics package to you: pathfindR <https://cran.r-project.org/package=pathfindR>
This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis
2018 Mar 12
0
pathfindR: An R Package for Pathway Enrichment Analysis Utilizing Active Subnetworks
Hello all,
I would like to introduce our group's new bioinformatics package to you: pathfindR <https://cran.r-project.org/package=pathfindR>
This tool is designed to improve pathway enrichment analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis
2009 Jun 20
1
string splitting and testing for enrichment
Hi List
I have data in the following form:
Gene TFBS
NUDC PPARA(1) HNF4(20) HNF4(96) AHRARNT(104) CACBINDINGPROTEIN(149) T3R(167) HLF(191)
RPA2 STAT4(57) HEB(251)
TAF12 PAX3(53) YY1(92) BRCA(99) GLI(101)
EIF3I NERF(10) P300(10)
TRAPPC3 HIC1(3) PAX5(17) PAX5(110) NRF1(119) HIC1(122)
TRAPPC3 EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89) RFX(121)
2011 Oct 24
1
Different symbols for select points
Dear R users,
I hope you can help me as you have done before.
I was wondering if I can make some of the points on my graph a different colour and symbol? Some of my soil samples are enriched and I wanted them to be shown with a red triangle and the samples which are not enriched I wanted to show with a blue square. I can't seem to find a way of doing this if there is a way?
My script:
2006 Aug 22
4
Successive subsets from a vector?
I'd like to pick every imbricated five character long subsets from a
vector. I guess there is some efficient way to do this without loops...
Here is a for-loop-version and a model for output:
VECTOR=c(1,4,2,6,5,0,11,10,4,3,6,8,6);
ADDRESSES=c();
for(i in 1:(length(VECTOR)-4)){
ADDRESSES[i]=paste(VECTOR[i:(i+4)],collapse="")
}
> ADDRESSES
[1] "14265"
2010 Jun 30
2
ggplot qplot bar removing bars when truncating scale
I'm having problems with this example, it is posted with reproduceable code
below, both with the normal 0-6 scale and the desired 3-6 scale (with bars
removed). How can I get the graph to have the desired 3-6 scale without
removing the bars. Thanks!
#Data
2008 Dec 09
2
motif search
Hi,
I am very new to R and wanted to know if there is a package that, given
very long nucleotide sequences, searches and identifies short (7-10nt)
motifs.. I would like to look for enrichment of certain motifs in
genomic sequences.
I tried using MEME (not an R package, I know), but the online version
only allows sequences up to MAX 60000 nucleotides, and that's too short
for my needs..
2006 Jan 11
2
Levelplot not working from file
I am trying to use the levelplot function from a command file.
Here is the code:
library(sp)
library(gstat)
library(lattice)
gatherData <- read.table("~/gather.txt", header = TRUE)
grd = makegrid(gatherData$x, gatherData$y, cell.size = 5)
k <- krige(z~x+y, ~x+y, data = gatherData, newdata = grd, nmax = 5)
levelplot(var1.pred~x+y, k, aspect = mapasp(k), main = "Predicted
2015 Mar 12
2
[LLVMdev] CFG Customization
Hi all,
I'm discovering LLVM and I want to build a customized CFG with
customized nodes (here BasicBlocks).
Simply, the purpose is to enrich CFG with some other informations.
What is the best way to do that ?
Please, tell me if I'm wrong (I'm not familiar enough with c++) but I
understand that :
- CFG is a GraphTraits<BasicBlock*>
- it's not allowed to inherit from
2005 Feb 05
2
Problem installing Hmisc
What am I doing wrong?
> install.packages("Hmisc")
trying URL `http://cran.r-project.org/src/contrib/PACKAGES'
Content type `text/plain; charset=iso-8859-1' length 47565 bytes
opened URL
==================================================
downloaded 46Kb
trying URL `http://cran.r-project.org/src/contrib/Hmisc_3.0-1.tar.gz'
Content type `application/x-tar' length
2011 Sep 13
2
GO & Protein Complex Analysis for Homo sapiens
Dear All,
I need to fetch GO ontologies for Homo sapiens with their mappings to
corresponding Uniprot identifiers. I would be using this information to
compare result from a clustering algorithm with existing protein complexes.
This would be a test to check how the clustering algorithm accurately
captures GO terms with respect to the known protein complexes. Can anyone
suggest a simple workflow
2005 Apr 04
2
locfit and memory allocation
Hello
I am getting memory allocation errors when running a function that uses
locfit within a for loop. After 25 or so loops, it gives this error.
"Error: cannot allocate vector of size 281250 Kb"
Running on linux cluster with a Gb of RAM. Problem never happens on my
OS X (less memory). The total data is 130 cols by 5000 rows
The first 129 cols are response variables, the 130th
2006 Oct 01
3
aggregate function with 'NA'
Dear r-help reader,
I have some problems with the aggregate function.
My datframe looks like
>frame
Day Time V1 V2
1 M 0 3 NA
2 M 0 4 NA
3 M 0 5 2
4 M 1 NA 4
5 M 1 10 6
6 T 0 4 45
7 T 1 4 3
8 T 1 3 2
9 T 1 6 1
I used the aggegate function to obtain the mean in V1 and V2 over the
grouping variable
Time and Day
2012 Sep 25
2
Help
For example, this station: http://radio.dyne.org:8000/ondarossa.mp3
has got a xspf file?
I obtain a message: Could not parse XSLT file when i try to open it
For the stations that I can't found in yp.xml
(e.g. http://212.162.68.230/1.mp3
http://212.162.68.230/2.mp3
http://212.162.68.230/3.mp3
http://stream15.top-ix.org/ondequadre )
it means they aren't on an official
2003 Jul 09
4
ignorepat doesn't work
Hi
in order to keep the dial tone after pressing 9 for 'outside line' I
have this in my extensions.conf
[localpstn]
ignorepat => 9
exten => _9[123456789]XXXXXXX,1,Dial,${PSTN}/${EXTEN:1}
exten => _9[123456789]XXXXXXX,2,Congestion
this is properly included in the handsets' context but the dial tone
disappears after pressing 9.
am I missing something?
thanks in advance
2015 Mar 12
2
[LLVMdev] CFG Customization
Hi John, thank you for your answer.
Sorry if I was not clear ^^'
I try to build a RCG (Resource Control Graph) which is a CFG with a
weight.
In my case, this weight corresponds to the number of heap allocations.
Then I want to add this weight to each node (then basic block) of this
graph.
I think that a CFG is a GraphTraits<BasicBlock*> then I suppose that
this RCG will be
a
2001 Apr 28
1
R for Mac Special Interest Group
R for Mac Special Interest Group
Alog with the forthcoming version 1.2.3 of R a new mailing list has been
activated. The list is intended to exchange ideas, impressions, give
suggestions etc on the portings of R for MacOS and MacOS X.
You can subscribe to the list going to its official page:
Go to the list page :
http://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac
To post a message to
2001 Jan 19
1
Web On line help and manual
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2004 Dec 03
1
isotonic regression
Hi,
Has anyone written code for isotonic regression on ordered rectangular
grids?
Nathan
Nathan Leon Pace, MD, MStat
University of Utah
Salt Lake City, UT 84132
Office: 801.581.6393
Fax: 801.581.4367
Cell: 801.558.3987
Pager: 801.291.9019
Home: 801.467.2925
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