search for: pathway

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 (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of th...

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 (Over-Representation Analysis). By utilizing the interaction information, the tool identifies most of th...

...i'm just not getting it, ?cast that is! So i'd really appreciate some ones patience to clarify this, using the reshape package, or any other approach. With sincere thanks in advance, Karl ## Runnable example ## The data.frame i have: library("reshape") my.df <- data.frame(pathway = c(rep("pw.A", 2), rep("pw.B", 3), rep("pw.C", 1)), cond.one = c(0.5, NA, 0.4, NA, NA, NA), cond.two = c(NA, 0.6, NA, 0.9, NA, 0.2), cond.three = c(NA, NA, NA, NA, 0.1, NA)) my.df ## The data fram i want: wa...

...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...

...yes'/> <vcpu id='2' enabled='no' hotpluggable='yes'/> <vcpu id='3' enabled='no' hotpluggable='yes'/> </vcpus> ... I'm able to hotplug vcpus, but when i want to unplug them i get the following: virsh # setvcpus pathway 3 --live virsh # setvcpus pathway 4 --live virsh # setvcpus pathway 2 --live error: internal error: unable to execute QEMU command 'device_del': acpi: device unplug request for not supported device type: qemu64-x86_64-cpu Does anyone know why it can't be unplugged ? Thanks. Brtnf -...

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)$"04010" [1] "MAPK signaling pathway" Marvellous! Except I want to do that when "04010" is assigned to a variable called path and I can't figure out how to do it! > path <- "04010" > > # the original and best > as.list(KEGGPATHID2NAME)$"04010" [1] "MAPK signaling pathway&qu...

Greetings all, I have two sets of data that I would like to investigate. The first is gene/genome related data given different 'cell-states'. The second set of data is relates the genes to a biological 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...

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 Registered Linux User Number 198875 ________________________________...

----- 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 unit='KiB'>16146944</memory> <currentMemory unit='KiB'>4147456</currentMemory> <!-- maxMemory unit=&...

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

I am trying to create a pie chart using 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(Path...

...so does the same. This happens about 1 out of every 5 records or calls. This only stated happening since updating the CVS from about the last 2 or 3 days. It was just pointed out tp me today on an outgoing call. Anybody ever hear of this? -- 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 Registered Linux User Number 198875 ________________________________...

Hello, Is there a convenient way to import RDF/OWL data into R? I'm interested in importing 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 h...

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", labels=c("Amino Acid", "Cofactors and Vitamins", "Carbohydrate", "Energy", "Lipid", "Peptide", "Nu...

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")) Start tag expected, '<' not found Warning: Parsing test/hsa04510.xml file failed, please check the file! That .xml file is...

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

...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? > > It would provide another pathway to suggest edits to the wiki without > requiring wiki edit permissions. > > For new documentation, e.g. layered project content from SIGs or > upstream documentation sources, I would think we'd want to skip a > conversion to/from Moin Moin and instead work directly in the sources...

...pathogen, Gibberella zeae, and I first used SAS to divide locus number with 10, 20, 30, or 40 on the fungal chromosome according to their location. I really want to see whether among the continual 10, 20, 30, or 40 locus has some expression pattern that different from rest genes. Because I know sigPathway (R package, pathway analysis with microarray data) can do this kind of job. What I use SAS to do is to subset locus in arbitrary genes numbers, such as 10, 20, 30, 40, or so on, and I hope to use sigPathway to analysis whether these genes chromosome location have effect on its gene expression. W...

...- (control) to be significantly different from zero, treatment A was significantly different, treatment B had no significant effect and there was a significant interaction between treatment A and treatment B. The interaction term is likely to be real. The treatments are on sequential steps in a pathway and treatment B may be blocking the effect of treatment A, i.e. treatment B alone has no effect because it blocks a pathway that is not active, treatment A reduces force via this pathway and treament B therefore blocks the effect of treatment A when used together. From what I understand, please c...