search for: enrich

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 [[alternativ...

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 the invol...

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 the invol...

...1(119) HIC1(122) TRAPPC3     EGR(26) ZNF219(27) SP3(32) EGR(32) NFKAPPAB65(89) NFKAPPAB(89) RFX(121) ZTA(168) NDUFS5     WHN(14) ATF(57) EGR3(59) PAX5(99) SF1(108) NRSE(146) TIE1     NRSE(129) I would like to test the 2nd column (each value has letters followed by numbers in brackets) here for enrichment via fisher.test. To that end I am trying to create two factors made up of column 1 (Gene) and column 2 (TFBS) where each Gene would have several entries matching each TFBS. My main problem just now is that I can't split the TFBS column into separate strings (at the moment that 2nd column...

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:            x <- c(0, 50, 100, 250, 500, 750, 1000, 1500, 2000, 2500, 3000)            y &l...

...+4)],collapse="") } > ADDRESSES [1] "14265" "42650" "265011" "6501110" "5011104" "0111043" "1110436" "104368" [9] "43686" Atte Tenkanen University of Turku, Finland [[alternative text/enriched version deleted]]

...;,"Impact"),c("Update knowledge and skills","Meet requirements for current position","Discover new job opportunities","Discover new job opportunities","Transition to a new job","Meet requirements for certificaiton","Personal enrichment","Update knowledge and skills","Meet requirements for current position","Meet requirements for certificaiton","Personal enrichment","Transition to a new job"))) colnames(data)=c("mean","variable","Q") data[,1]=...

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.. Thanks A

...x = 5) levelplot(var1.pred~x+y, k, aspect = mapasp(k), main = "Predicted 5m") It executes fine (it plots up) when I cut and paste to the command prompt but it seems to be missed (nothing occurs) when I call the source file. I am using OSX. Thanks for any help. Matt [[alternative text/enriched version deleted]]

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 BasicBlock (never seen in the project) Maybe it...

...rginia Department of Psychology USPS: P.O.Box 400400 Charlottesville, VA 22904-4400 Parcels: Room 102 Gilmer Hall McCormick Road Charlottesville, VA 22903 Office: B011 +1-434-982-4729 Lab: B019 +1-434-982-4751 Fax: +1-434-982-4766 WWW: http://www.people.virginia.edu/~mk9y/ [[alternative text/enriched version deleted]]

...test to check how the clustering algorithm accurately captures GO terms with respect to the known protein complexes. Can anyone suggest a simple workflow with the requisite packages? I am trying to find out to fetch GO ontologies for homo sapiens with bioconductor but most packages are designed for enrichment analysis. Am I missing something here? Any help would be greatly appreciated. Thanks a lot in advance. -- Warm Regards, Sandeep Amberkar BioQuant,BQ26, Im Neuenheimer Feld 267, D-69120,Heidelberg [[alternative HTML version deleted]]

...ion? (or is that too slow?) Many Thanks in Advance! Mike Mike Hickerson University of California Museum of Vertebrate Zoology 3101 Valley Life Sciences Building Berkeley, California  94720-3160  USA voice 510-642-8911 cell: 510-701-0861 fax 510-643-8238 mhick@berkeley.edu [[alternative text/enriched version deleted]]

...e$Day,frame$Time),mean) Group.1 Group.2 Time V1 V2 1 M 0 0 4.000000 2 2 T 0 0 4.000000 45 3 M 1 1 10 5 4 T 1 1 4.333333 2 > I hope my description makes sense and appreciate any help. Yours Frank [[alternative text/enriched version deleted]]

...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 database ? because I can hear them! so they exist! The project to enrich the APIs is a long term plan? Because I think this is a very good project and it needs APIs!! Thanks again for your disponibility and sorry for my english! 2012/9/25 R?cker Thomas <thomas.ruecker at tieto.com>: > On 25/09/12 16:42, renato fringuello wrote: > > Ok Thomas, I understo...

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

...st way to do it. > > Regards, > > John Criswell > > > On 3/12/15 12:41 PM, rubiano wrote: >> 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 fro...

...ficial page: Go to the list page : http://www.stat.math.ethz.ch/mailman/listinfo/r-sig-mac To post a message to this list just send a mail to r-sig- mac at stat.math.ethz.ch Stefano -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 819 bytes Desc: not available URL: <https://stat.ethz.ch/pipermail/r-announce/attachments/20010428/f43a25e6/attachment.bin>

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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 [[alternative text/enriched version deleted]]