Bioconductor Forum

div class="preformatted">Hi All, I am using 'topGO package for GO enrichment analysis in non model organisms. I found the tool really intuitive and versatile as far as the statistical test are concerning. However, I was wondering

GO

updated 11.2 years ago • artur

I get this error : ```r Genes_up_d5_vs_d0_KEGG <- enrichKEGG(gene=Genes_up_d5_vs_d0$entrezgene_id, organism = "mmu", qvalueCutoff = 0.05) Reading KEGG annotation online: fail to download KEGG data... Error in download.KEGG.Path...species) : 'species' should be one of organisms listed in 'http://www.genome.jp/keg…

KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db

updated 2.3 years ago • Milan

Hi Bioconductor community, I am trying to build an Org.db for a "not-so" model organism that lacks an entry in AnnotationHub(). For this I used makeOrgPackageFromNCBI, and although it took a very long time...Hi Bioconductor community, I am trying to build an Org.db for a "not-so" model organism that lacks an entry in AnnotationHub(). For this I used makeOrgPackageFromNCBI, and although it t…

OrganismDbi makeOrgPackageFromNCBI

updated 23 months ago • dissikratzl

and this year I submitted the application form for R. Google asks "Are you an established or larger organization who would like to vouch for a new organization applying this year?" so I can do that for you if the Bioconductor

updated 12.7 years ago • Guest User

Resourcerer"), "temp")) *# > [1] "README"* annot <- getResourcerer( "affy_HG-U133_Plus_2.zip", organism = "human", destDir = file.path(.path.package("Resourcerer"), "temp"), baseUrl = "ftp://occams.dfci.harvard.edu/pub/bio/tgi/data...resourcerer object is correctly created resourcerer <- getResourcerer( "Agilent_Human1_cDNA.zip", organism = "human", destDir = file.path(.pa…

Annotation Organism Annotation Organism

updated 14.4 years ago • Guillaume Tiberi

Please find in the attached PDF more information about this event, including the scientific program. Organizes: COST Action SeqAhead Local organizers: Ana Conesa, Ignacio Medina, Joaqu?n Dopazo Venue: Centro de Investigaci?n

updated 13.7 years ago • Ana Conesa

seem to be no worm annotations in the KEGG package. Are there any plans to add them? Or perhaps a organism-specific annotation package for worm? If not, does anyone know where I can download them (I don't see any KEGG annotations

Annotation Annotation

updated 17.3 years ago • Sara Calafell Gosline

and kegg pathways (ko....). Can the keggrest package do it? I found only examples specifying the organism name, but I have many different bacterial species... Is it possible concurrently doing a search for more species? Thanks

keggrest kegg keggorthology

updated 11.1 years ago • francesca.defilippis

Hello, I have an in-house assembly for a non-model organism. I am planning to forge a BSgenome data package. I have 2 questions regarding that: 1. As the assembly is not yet published

BSgenome

updated 4.6 years ago • aybuge.altay

Hi, I'm running the enrichPathway function: x<-enrichPathway(gene=df$name, organism = "fly", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2, universe, minGSSize = 10, maxGSSize = 500, readable = FALSE

enrichPathway ReactomePA

updated 5.6 years ago • DataFanatic

running gseDO() from the DOSE package but, I just realised I can't or I don't know how to change the organism from human to Mouse. You can see the following script and the error. y <- gseDO(geneList, nPerm = 500, minGSSize = 15, pvalueCutoff

ClusterProfiler

updated 6.2 years ago • raianbio

expressed genes from an rna-seq analysis. Also, I have a two-column annotation file for the organism with the columns being gene and goterm. please guide me towards a bioconductor package or any other tool that I could

Annotation Organism Annotation Organism

updated 13.0 years ago • Alpesh Querer

a 2x2 contigency table?   In addition to, I have 28031 genes (there are lncRNA), I should organize table for each gene

rnaseq differential gene expression

updated 9.2 years ago • elhamdallalbashi

UniGene" as an URL for UG, but this isn't >working A quick fix is to use getSrcUrl("all", organism = "Homo sapiens") (for human) instead of using getOption for source urls. We will change the options and have the pakcage...now subfolders "Homo_sapiens" etc. > > > >In your function getUGBuilt > >function (organism, url = "ftp://ftp.ncbi.nih.gov/rep…

Cancer Organism Cancer Organism

updated 20.2 years ago • John Zhang

PDF manual ---“How To Use GOstats and Category to do Hypergeometric testing with unsupported model organisms”. I got the following error in hyperGTest():  “getUniverseHelper(probes, datPkg, entrezIds) :   After filtering...2 #The gene ids used to map to GO are set as “1,2….”(numeric) >goFrame=GOFrame(goFrameData,organism="test") >goAllFrame=GOA…

GOstats

updated 10.8 years ago • doodlehzq

I a trying hard to make a proper txdb object that I can ultimately use with `gDNAx` package. I raised a separate issue [here][1] but I have realized that it's not gDNAx's problem but is actually about how the txdb object is created. I have downloaded the FASTA file and GTF file from ToxoDB from [here][2] and I have been trying hard to make a proper txdb object on which when I run `seqlevelsStyle`…

txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx

updated 11 months ago • rohitsatyam102

I have a problem when I try to use GOSemSim to calculate the GO semantic similarities between yeast proteins. geneSim("852494", "854869", ont = "MF", organism="yeast", measure="Resnik") return below result: \[1\] NA Warning messages: 1: In is.na(go) : is.na() applied to non-(list or vector) of...the GO semantic similarities between yeast proteins. geneSim("852494", "854869", ont = "MF",…

GOSemSim yeast

updated 10.8 years ago • horcsct

to look at arabidopsis, then you may already have > everything you need. And if you need another organism, you probably > want to look 1st at making an org package using > makeOrgPackageFromNCBI(). And if for some reason...you want to expose > some entirely new database resource (IOW you don't want to make an > organism package but something else entirely), th…

Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi

updated 12.3 years ago • Sashi

Hi all,  I just wanted to ask a general question about the best way to go about carrying out differential expression analysis between multiple groups. I have a microarray data set that has 10 different groups (i.e, 10 organs in one age group). Essentially what I want to do is find a common core set of differential expressed genes across every single group. I have created contrasts by su…

multiple groups differential gene expression microarray

updated 8.1 years ago • A

At present I am using the Development version of the package (see below) because I have a "non-model" organism (mosquito, Anopheles), and it seems I need to use the latest/development version to use the Kegg gene IDs for my organism

Organism convert pathview Organism convert pathview

updated 12.2 years ago • Hilary Smith

Hello, I need to map GenBank protein ID's to corresponding Uniprot ID's from non-model organisms (e.g. ACF95883.1 = https://www.uniprot.org/uniprotkb/B5ATG2/entry = SOX9). I am struggling to find tools to do so, could

UniProt.ws AnnotationDbi

updated 17 months ago • georgii.vdovin

other informations or transcription data. I used EnrichR but since it does not have an option for organism, I have some human pathways as answer for mouse genes. I just want to do a hypergeometric test to identify enriched

R GSEA rna-seq scRna-Seq

updated 6.8 years ago • hamza_karakurt

anyone give me some advice on this task? Or indicate a material do read? In case it is relevant, the organism is Bos taurus. Thanks in advance, Fernando </div

Organism Bos taurus Organism Bos taurus

updated 14.8 years ago • Biase, Fernando

annFUN.db, affyLib = affyLib) what if there is no annotation database available for that particular organism in bioconductor? Can someone tell me if there is any alternative available to use instead of the annotation databases

topGO affy

updated 7.8 years ago • User

pre> queryEncode(biosample = "ES-E14", target = "CTCF", file_format = "bed", assay = "ChIP-seq", organism = "Mus musculus", fixed = FALSE)</pre> returns NULL, although [here](https://www.encodeproject.org/experiments/ENCSR362VNF

encodexplorer

updated 9.8 years ago • liz.ingsimmons

analysis on the data. There is no built-in package for the two bacteria that I work on, so I made organism packages using makeorgpackagefromncbia(). The problem is, the packages made this way do not contain 'egGO2ALLEGS

ontology edger limma ncbi organism package

updated 5.7 years ago • babak.loghmani

div class="preformatted">Dear all I'm working with an unsupported organism. However I have a table of PFAM annotations for my genes and would like to make a GeneSetCollection out of it (to use

Organism Organism

updated 11.5 years ago • Fabian Grammes

<div class="preformatted">Hi, We are currently trying to develop a library to deal with nylon arrays. I wanted to build an annotation package for our chip, but i have an error with GO. Here is the log : $> mySrcUrls <- c(EG="ftp://ftp.ncbi.nih.gov/gene/DATA",UG="ftp://ftp.ncbi.nih.gov/rep ository/UniGene/Homo_sapiens/Hs.data.gz") $> myBase <- "/home/jtextori/D…

Annotation GO Organism annotate AnnBuilder Annotation GO Organism annotate AnnBuilder

updated 19.9 years ago • TEXTORIS Julien

Hi I am new to clusterprofiler and R. I have read the vignette also. I could use the groupGO easily on the set of genes but enrichGO throws an error saying "Error in enrichGO(gene = cephalexinlist, organism = "ecolik12", ont = "BP", : unused argument (organism = "ecolik12")". The script is below. What am I doing wrong here? Please any help will be appreciated. Many thanks in advance. library(cl…

clusterprofiler

updated 8.0 years ago • taiyebzahir13

supported by the Chan Zuckerberg Initiative's EOSS program, has joined The Carpentries as a member organization to ensure excellence in instruction and to develop infrastructure to create and maintain high-quality, pedagogically

teaching Carpentries

updated 3.1 years ago • Maria Doyle

sequence and to save them to then look for overlaps of these with mismatched nucleotides between two organisms for designing specific strain qPCR probes and primers. I've tried saving them as a data frame from findPalindrome

findPalindrome() Palindrome

updated 4.6 years ago • meyerlaker

<div class="preformatted">Dear Darrell, We (Vincent Zimmern and me) are currently implementing this functionality. By March 18th, (the next Bioc release development deadline) we should have it integrated in the new easyRNASeq version (1.6.x). As part of that development, we have(are) developed(ing) unit tests that actually reproduce that functionality. Once sufficiently confident that it w…

Annotation Organism easyRNASeq Annotation Organism easyRNASeq

updated 12.8 years ago • delhomme@embl.de

analyzing peptide array data; integrating the data to yield an integrative map of factors leading to organ rejection. This work will be done in collaboration with the Medical University of Vienna (Prof. Rainer Oberbauer) and...for peptide arrays \*) Establishing a data platform for integration of factors leading to kidney organ rejection __Qualifications__ \*) Knowledge about  …

bioinformatics protein variantannotation data integration Job

updated 9.1 years ago • stephan.pabinger

one gives the error keggID <- "05213" tmpXML <- "testKGML1.xml" retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, method="wget") tmpGraph1 <- parseKGML2Graph(tmpXML, genesOnly=FALSE) plotKEGGgraph(tmpGraph1...complicated graph keggID <- "04810" tmpXML <- "testKGML2.xml" retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, method="wget") …

Pathways KEGGgraph Pathways KEGGgraph

updated 15.4 years ago • Robert M. Flight

srcUrls= mySrcUrls, baseMapType= myBaseType, otherSrc= myOtherSrc, pkgName ="myPkg", pkgPath=myDir, organism="human", version ="1.9.0", makeXML= TRUE, author=list(author="MGG", maintainer="m.gardiner-garden@garvan.org.au"),fromWeb...srcUrls= mySrcUrls, baseMapType= myBaseType, otherSrc= myOtherSrc, pkgName ="myPkg", pkgPath=myDir, organism="human", version ="1.9.0", makeXML= TRUE, author=list(aut…

GO Organism AnnBuilder PROcess GO Organism AnnBuilder PROcess

updated 21.3 years ago • Margaret Gardiner-Garden

but I'm really stuck. I am running enricher (the generic version because I'm not using a model-organism) and I am supplying my own list of GO terms. I run it like this: ```r ego_bp_aga <- enricher(gene = aga_genes, TERM2GENE = go_terms

clusterProfiler GO.db

updated 3.5 years ago • Lucía

to add inches to the male package, as well as thicken and improve the muscular appearance of your organ. Try it today. "After I started taking POWER Gain++, I've gained more than 2 inches in just weeks. Sharon now comes almost every

updated 17.0 years ago • Elijah Mathis

I have microarray data to analyze with 3 factors: Genotype (wt, mut), Treatment (C, T), and Organ (s, r), each in 3 replicates. I found the guide for limma, I am just confused about how to "makeContrasts" to get all levels of...I have microarray data to analyze with 3 factors: Genotype (wt, mut), Treatment (C, T), and Organ (s, r), each in 3 replicates. I found the guide for limma, I am just conf…

interactions 3factors limma Microarray

updated 4.8 years ago • Dan

untill I try this command:      GOenr = GOenrichmentAnalysis(moduleColors, allLLIDs, organism = "mouse", nBestP = 10) It gives the following error:      Error in get(name, envir = asNamespace(pkg), inherits = FALSE

wgcna

updated 7.7 years ago • yepingsun80

Hello, I'm using GOstats (version 2.42.0) to perform GO enrichment analysis in a non-model organism. The input data was obtained from the DE analysis of RNA-Seq data. For the analysis I used an own gene universe, as well

GOstats

updated 8.1 years ago • martis.mihaela

I can not define single "ndups", I'm not sure if I can still use this function, or I have to re-organize the data for using this function? Are there other functions I can use to solve this problem? Any suggestions appreciated

Microarray limma Microarray limma

updated 17.4 years ago • Yi Zou

I tried to create a TxDd object using the makeTxDbFromEnsembl function, but got the following error: txdb = GenomicFeatures::makeTxDbFromEnsembl(organism = "Homo sapiens") Fetch transcripts and genes from Ensembl ... OK Fetch exons and CDS from Ensembl ... OK Fetch chromosome names...function, but got the following error: txdb = GenomicFeatures::makeTxDbFromEnsembl(organism = "Homo sapie…

genomicfeatures

updated 7.5 years ago • kaur.alasoo

nbsp;package, how one could list the different database versions that exist for a specific organism (let's say mouse)? • Question 2: The tutorial mentions "The transcripts function can be used with return.type="DataFrame

ensembldb tximport salmon

updated 7.6 years ago • user31888

wheat array, with some very ancient annotations included. I have been looking, and many sequenced organisms have a xxx.db annotation package that is used in conjunction with annotationDBi. I have found the wheatcdf, which

Annotation cdf AnnotationDbi Annotation cdf AnnotationDbi

updated 13.5 years ago • Guest User

<div class="preformatted">Dear all, I am wondering whether there are any documentation for adding custom annotations (eg: transcription factor enrichment, mirna targets...) for unsupported organisms  and do enrichment analysis using GOstats package? So far I was able to find only this vignette pdf (http://www. bioconductor.org...adding custom annotations (eg: transcription factor …

Transcription miRNA GO Transcription miRNA GO

updated 13.4 years ago • sudeep s

NCTC1168) from the UCSC genome browser,but discovered that UCSC genome browser did not have the two organisms; however, the two organisms are hosted in UCSC Microbial Genome Browser. I wonder if there is any plan to support UCSC

GenomicFeatures GenomicFeatures

updated 11.9 years ago • Guest User

this over in late January. So it would be the initial setup and population that would be required. Organization: - we need someone (volunteers please take a giant step forward) to organize some mechanism for keeping track of

GO GO

updated 24.1 years ago • rgentleman

<div class="preformatted"> Hi, when using retrain() in the gene2pathway library I get the following error: library(gene2pathway) > retrain() Retrieving KEGG information via SOAP ... xmlns: URI SOAP/KEGG is not absolute xmlns: URI SOAP/KEGG is not absolute Fehler in gene2pathway:::buildTrainingSet(minnmap = minnmap, level1Only = level1Only, : Organism 'hsa' is unknown in KEGG! Ple…

Organism hgu95av2 gene2pathway Organism hgu95av2 gene2pathway

updated 13.5 years ago • Guest User

preformatted">Hi all, I have downloaded the KGML files of for all the pathways of some organisms . I want to automate the process of constructing the metabolic networks of these organisms. In a directory by name

Pathways Network PROcess Pathways Network PROcess

updated 15.9 years ago • anupam sinha

FALSE, quote=FALSE) ABPkgBuilder(baseName=file.path(myDir, "AnnDan"), srcUrls=getSrcUrl("ALL",organism='mouse'), baseMapType = 'ug',otherSrc = NULL, pkgName="mu11KABannot", pkgPath=myDir, organism = "mouse",version = "1.3.0", makeXML

Annotation GO Organism Annotation GO Organism

updated 21.6 years ago • Mayte Suarez-Farinas

note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================</div

updated 16.6 years ago • Manel, Nicolas

all, I am using the KEGGgraph package to construct metabolic networks of various organisms and study their topological properties.My query though is : Can the package KEGGgraph be used to construct a weighted

Pathways graph KEGGgraph Pathways graph KEGGgraph

updated 16.0 years ago • anupam sinha

http://www.bioconductor.org/packages/release/bioc/html/goTools.html). Since I am using a non model organism I build my own organism package using [AnnotationForge](http://www.bioconductor.org/packages/release/bioc/html...file of my package it is obvious that the org.Psp.FOBEG1.egGO is missing. Looking in other organism packages (e.g. org.Hs.eg.db) I understood that org.Xx.egGO is a "Go…

goprofiles AnnotationForge Bimap GO

updated 11.2 years ago • artur

2014) and stored in Biostrings objects. See Tang et al. (2014) BMC Genomics 15:312 Version: 4.0 organism: Medicago truncatula A17 common\_name: Barrell medic provider: JCVI provider\_version: v4 release\_date: 2014 release...source\_url: ftp://ftp.jcvi.org/pub/data/m\_truncatula/Mt4.0/Assembly/JCVI.Medtr.v4.20130313.fasta organism\_biocview: Medicago\_truncatula BSgenom…

bsgenome biostrings Gviz

updated 10.2 years ago • gtho123

Hello all, about a year ago I wrote a simple wrapper for `KEGGREST` to generate a collection of modules and pathways for a particular organism in the form of `.gmt` file, which is very useful for gene set enrichment tools like `fgsea`. Coming back to use the code a year later, I discovered that `keggGet` command started to fail when trying to retrieve modules (but not pathways). For examp…

keggrest software error pathways modules kegg

updated 5.7 years ago • predeus

uuiijkt-l-u Nucleomics Core User Meeting On Thursday March 21st 2013, VIB Nucleomics Core will organize their yearly user meeting at the "Provinciehuis" in Leuven. Anniversary Meeting Since this is the first time that...mainly from an academic setting (Ph.D. Students, Post-Docs, Group-Leaders) but also from profit organizations, in Belgium and other parts in Europe. Visit our website for mor…

Sequencing Microarray Sequencing Microarray

updated 12.8 years ago • Rudy van Eijsden

jcc/blob/master/R/fitAlpineBiasModel.R fitAlpineBiasModel <- function(gtf, bam, organism, genome, genomeVersion, version, minLength = 600, maxLength = 7000, minCount = 500, maxCount = 10000, subsample = TRUE, nbrSubsample...txdb <- tryCatch({ e…

Alpine jcc

updated 6.3 years ago • bioinagesh

the [2023 Bioconductor conference][1] (BioC2023), to be held in Boston August 2-4, is looking for organizers to help in planning the event. Participation involves attending approximately monthly remote meetings (more

BioC2023 Bioconductor community

updated 2.9 years ago • Maria Doyle

with http://www.abalone.ca? We would also love to feature an article you or someone else in your organization has written about the web, if you would do the same for us. Thanks so much! Sincerely, Courtney Heard courtney at

updated 18.1 years ago • Courtney Heard

option, but I'm not quite sure how to use this (I'm terrible at R). I'm working on a non-model organism that does not have UTRs encoded in the GTF file or else I could likely use a simpler method. Any help would be greatly

genomicfeatures

updated 6.8 years ago • courtney.stairs