search for: pathways

...analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways. pathfindR also creates pathway diagrams with the involved genes colored by change values. (this is achieved using the bioconductor package pathview) Finally, the package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and...

...analysis by firstly identifying active subnetworksin differential expression/methylation data using a protein-protein interaction network. It then performs pathway enrichment analysis (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of the involved pathways. pathfindR also creates pathway diagrams with the involved genes colored by change values. (this is achieved using the bioconductor package pathview) Finally, the package allows for clustering of enriched pathways and establishment of representative pathways. This allows for further abstraction and...

Esteemed UseRs, This must be embarrassingly trivial to achieve with e.g., melt() and cast(): deduplicating records ("pw.X" in example) for a given set of responses ("cond.Y" in example). Hopefully the runnable example shows clearly what i have and what i'm trying to convert it to. But i'm just not getting it, ?cast that is! So i'd really appreciate some ones

...problems with developing this vignette and its example datasets: 1) I am unsure if my use of the extdata file is appropriate. This seemed to be the best directory name and location to place my example files, according to the aforementioned Hadley Wickham reference. 2) I am unsure how to make the pathways relative, instead of absolute, as I have them currently. This example code does not run automatically, as you can see. Instead, I have it under an R chunk of eval=FALSE so that it is simply listed there for the users to test themselves. After running the example code, the users can also check that...

Hi, i'm playing a bit around with vcpus. My guest is Windows 10 1903. This is the excerpt from the config: ... <vcpu placement='static' current='2'>4</vcpu> <vcpus> <vcpu id='0' enabled='yes' hotpluggable='no'/> <vcpu id='1' enabled='yes' hotpluggable='yes'/> <vcpu id='2'

Hi Dumb question time again, for which I apologise. I have a variable that contains the following numerical text "04010". This is the name to access a list: > as.list(KEGGPATHID2NAME)$"04010" [1] "MAPK signaling pathway" Marvellous! Except I want to do that when "04010" is assigned to a variable called path and I can't figure out how to do it!

...pathway. /(I think in pictures so here goes.)/ *dataframe1* gene, cell-state1, cell-state2 gene1, x1, y1 gene2, x2, y2 gene.x, ..., ... *dataframe2* pathway1, gene-x1, gene-x2, ... pathway2, gene-y1, gene-y2, ... What I want to do is, see if 'cell-state1' (in-)activates different genes / pathways from 'cell-state2.' Furthermore, I would like to test for correlation /(t-test and maybe graphing)/ between the cell-states 1 Vs 2 for specific pathways. My question is, which commands or method would allow me to do this most easily/efficiently: *merge* or using *dummy variables*? -- View...

Am I doing something wrong? I can't get this dial command to timeout.... Dial(Zap/g1/xxxxxxx,20) -- Gary White admin@netpathway.com Network Administrator Internet Pathway 105 D East Church Street Voice: 601-776-3355 P. O. Box 777 Fax: 601-776-2314 Quitman, MS 39355

----- On Feb 15, 2020, at 12:47 AM, Marc Roos M.Roos@f1-outsourcing.eu wrote: > Would you mind sharing your xml? I have strange high host load on idle > windows guest/domain <domain type='kvm'> <name>pathway</name> <uuid>8235e5ae-0756-4286-5407-9fa02d372046</uuid> <description>Pathway Studio Dietrich</description> <memory

Hi, I have a CSV file where each row has at least 20 columns and some rows have up to 30 columns of data. When I use the command, Pathways<-read.table('MetaCycSample3.csv',sep=',',header=FALSE,quote='"') anything past the 21st column gets kicked down to a new row. How can I fix this? Thanks, -Nina

Hello, Does anyone know of a way of finding all the nodes that are between a pair of specified nodes in the excellent graph package (R vers 2.5.0). I have a class(graphAM) object and need to determine all possible pathways in this object. Here's an example: In the simple case of a--b--c (where -- denotes "conected to") the list of all pathways would be: ab ba abc cba cb bc. Thanks in advance, Dan

...g rpy2 of the following data Pathway Occurrences A 10% B 50% C 20% E 10% filename = './testing.png' grdevices = importr('grDevices') rdevices.png(file=filename, width=1200, height=800) dataf = Robjects.DataFrame({'pathways':Robjects.StrVector(Pathways), occurrences' : Robjects.FloatVector(Occurrences) }) pie = ggplot2.ggplot(dataf)+ \ ggplot2.aes_string(x='',fill='pathways',weight="amounts")+\ ggplot2.geom_ba...

Guys, I have a problem that I can seem to run down. I'm running CVS-HEAD-09/10/04-18:14:15 on a Celeron 500 with an Intel chipset motherboard. The audio from my GS phone to * is sometimes decoded at about twice the normal speed on some outgoing calls. Also.when recordind a message to * from the GS it also does the same. This happens about 1 out of every 5 records or calls. This only

...mporting BioPAX/SBPAX data into R to make them available for a wider audience. One exciting application would be to use pathway data to explain differential microarray measurements by identifying upstream nodes that are likely involved in causing the differences. This could also be used to validate pathways or to estimate concentrations or kinetic parameters. If no convenient method to import RDF/OWL exists, I would be happy to take the lead in creating a light-weight R package based on rjava and OpenRDF Sesame Rio that could query RDF/OWL data and turn the results into data frames. Thanks!...

I have following codes for ggplots. The legends are given in the plot do not match with the values specified in the codes given below. Your helps highly appreciated. Greg library(ggplot2) p <- ggplot(a,aes(x=NO_BMI_FI_beta ,y=FI_beta ,color= Super.Pathway))+ theme_bw() +theme(panel.border=element_blank()) + geom_point(size=3) p2<-p+scale_color_manual(name="Super.Pathway",

Hi, I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. The following error occurs after this command line below: >pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native = F, same.layer = T, species = "hsa", kegg.dir = "test", out.suffix = "up"))

hello, can i authenticate samba to pam and then ldap? thank you. --David Weise OIT Rider University "The real race is not on the hot, paved road, the torturous off-road course or the smooth-surface velodrome. It is in the electrochemical pathways of your mind."--Alexi Grewal

On Mon, Apr 11, 2016 at 10:37 AM, Karsten Wade <kwade at redhat.com> wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > On 04/11/2016 09:18 AM, Jim Perrin wrote: >> What are the thoughts or concerns about this sort of workflow >> change? > > Any chance Moin Moin can store wiki source in git and sync > automatically with a central git repository?

...hist(statList$pval,breaks=seq(0,1,0.025),xlab="p-value",ylab="Frequency",main="") set.seed(1234) YANG <- runSigPathway(yy,20,500,Y,p,nsim=100,weightType="constant",ngroup=2,npath=10,verbose=F,allpathway=F,alwaysUseRandomPerm=F) #write.table(YANG$df.pathways[1:25, ]) write.table(YANG$df.pathways[1:25,],quote=F,sep="\t",file="chr1_sig.txt") YANG$list.gPS[[1]] save.image("chr1_sig")

Gday, This is a repost since I only had one direct reply and I remain mystified- This may be stupidity on my part but it may not be so simple. In brief, my problem is I'm not sure how to extract parameter values/effect sizes from a nonlinear regression model with a significant interaction term. My data sets are dose response curves (force and dose) for muscle that also have two