Bioconductor Forum

Is there documentation for creating annotation objects from scratch, i.e., for unsupported organisms? I am analyzing expression data for an organism that is not on the list at bioconductor.org. How would one go about

Annotation Annotation

updated 16.6 years ago • Michael Muratet

<div class="preformatted">Does anyone have any experience with building an Annotation package for organisms other than Human, Mouse, or Rat? With AnnBuilder or any other package? In the documentation for the ABPkgBuilder{AnnBuilder...div class="preformatted">Does anyone have any experience with building an Annotation package for organisms other than Human, Mouse, or Rat? With AnnBuilder…

Annotation AnnBuilder Annotation AnnBuilder

updated 20.3 years ago • Bornman, Daniel M

<div class="preformatted">Does anyone have any experience with building an Annotation package for organisms other than Human, Mouse, or Rat? With AnnBuilder or any other package? In the documentation for the ABPkgBuilder{AnnBuilder...div class="preformatted">Does anyone have any experience with building an Annotation package for organisms other than Human, Mouse, or Rat? With AnnBuilder…

Annotation AnnBuilder Annotation AnnBuilder

updated 20.3 years ago • Bornman, Daniel M

have easily be done within R, for example. the gds (data sets) table contains two fields related to organisms: sqlite GEOmetadb.sqlite 'pragma table_info(gds)' | grep organism # 7|platform_organism|TEXT|0||0 # 10|sample_organism...table does not contain any such field: sqlite GEOmetadb.sqlite 'pragma table_info(gse)' | grep organism the gpl (platform) table contains one such f…

Cancer Breast Organism GEOmetadb Cancer Breast Organism GEOmetadb

updated 16.7 years ago • Wacek Kusnierczyk

well, but I have an annoying issue. The package is said to include a database to optimise for 200 organisms. However, the abbreviation used to specify which organism appears to be non-standard and without documentation

GeneGA

updated 11.0 years ago • tomas.bjorklund

Dear bioconductor assistance group, I am performing a specific research in leaf-cutting ants; and I will need to build the organism package of Atta cephalotes and Acromyrmex echinatior wide-genome package for a RNA-seq anlysis. I need that non-model...group, I am performing a specific research in leaf-cutting ants; and I will need to build the organism package of Atta cephalotes and Acromyr…

annotation deseq2

updated 6.9 years ago • estevemp

Howver, when running mutSignature, it errored out and I traced the problem to be missing the "organism" term in the slotNames of the BSgenome object. I tried to resinstall this package a few times, same problme, "organism

Bioconductor

updated 7 weeks ago • ubjw24

I have RNA-Seq data from a prokaryotic non-model organism (*Microbacterium*) and I am doing a gene set enrichment analysis. I mapped my amino acid sequences to KO annotations...first. I then managed to do the gene set enrichment analysis by using `organism = 'ko'`. ``` gse_kegg <- gseKEGG( geneList = geneList, organism = 'ko', minGSSize = 120, pvalueCutoff = 0.05, verbo…

clusterProfiler KEGG GeneSetEnrichment

updated 4.1 years ago • makrez

abs(geneList) > 2\] > <span style="line-height:1.6">ggo <- groupGO(gene = gene, organism = "human", ont = "BP",level = 3, readable = TRUE)</span> __Error in groupGO(gene = gene, organism = "human", ont = "BP", level = 3,  : __ __unused...argument (organism = "human")__    I don't understand why there should be an er…

error

updated 9.2 years ago • zhaoxiao

I want to analyse RNA-Seq data for non-model organism using DESeq pacakge, organism is : Rhodnius proxilus http://metazoa.ensembl.org/Rhodnius\_prolixus/Info/Annotation

bsgenome

updated 8.8 years ago • minie

I am analyzing a mouse microarray data by using SPIA package. At the end, I need to input an organism name so the package can recognize it. res=spia(de=HIF1a,all=HIF1a1,organism="hsa",nB=2000,plots=F,beta=NULL, combine="fisher

Microarray Organism SPIA Microarray Organism SPIA

updated 14.3 years ago • Jing Huang

Dears all, I need get the reactions for a organism. I am using KEGGREST for that. In the manual of KEGGREST says that I can use keggList(database, organism), but I am trying...BiocInstaller, but nothing works. I wonder if is not possible to obtain the reaction for specific organism with KEGGREST, or exist other solution? Thanks

keggrest

updated 9.6 years ago • kjboteroo

<div class="preformatted"> I have a query about the format of the organism name to use in ABPkgBuilder and getSrcUrl functions of AnnBuilder. It seems in some functions organism should be the official name (eg Mus Musculus) but in other functions it should be the common name (eg mouse). The vignette states that you can get the src URls by calling mySrcUrl <- getSrcUrl("all","mouse"…

Microarray Organism Mus musculus AnnBuilder Microarray Organism Mus musculus AnnBuilder

updated 20.5 years ago • Christopher Wilkinson

BSge nome/inst/doc/BSgenomeForge.pdf To get enriched GO, you will need org.*.eg.db package for your organism. I think the Bioconductor Core team has built the packages for different organisms using AnnotationDbi. I cced bioconductor...R though. I just started a project to study multiple transcription factors in a non-mainstream organism, Toxoplasma gondii (a relative of Plasmodium). I do have a…

Transcription Annotation GO AnnotationData Organism BSgenome biomaRt BSgenome ChIPpeakAnno

updated 14.6 years ago • Julie Zhu

data.frame(frame$go_id, frame$Evidence, frame$gene_id) > goFrame = GOFrame(goframeData, organism = "Rattus norvegicus") Error in .testGOFrame(x, organism) : All of the Evidence codes in your data.frame object must be legitimate

GO Organism rat2302 AnnotationDbi GO Organism rat2302 AnnotationDbi

updated 12.7 years ago • Guest User

BSgenome.Nta"))        bg.logn = makeBackground(pwms.denovo, organism=BSgenome.Nta, type="logn") and I am getting error like this Error in getPromoters(organism) :   Promoter sequences

r pwmenrich

updated 7.9 years ago • prp291

Hi all, I'm new to R and have some very basic questions about using GOstats with a non-model organism. I'm trying to use the tutorial by Marc Carlson "How to Use GOstats and...with unsupported model organisms." I've created...function "toTable", for signature "data.frame" Do I have to create some sort of database for this organism first? If so, what is it's format? Any suggestions would be m…

GO Organism GO Organism

updated 14.8 years ago • Maureen J. Donlin

Prepare the 'metadata' data frame ... Error in GenomeInfoDb:::lookup_tax_id_by_organism(organism) : Solanum_lycopericum: unknown organism. Please use 'loadTaxonomyDb()' to see viable genus/species and taxonomy IDs

annotation

updated 5.1 years ago • anuranjansrathore

are based on commercial platforms. How can I do GSEA analysis for the customized array of no model organisms using existed packages? For example, an array constructed based on unigenes, and the organism's genome has not yet

GO GO

updated 16.4 years ago • Pengcheng Yang

on my microarray results, and have not done this before. We have a cDNA array for a non-model organism. The manufacturers of the array have provided annotations, so I have Accesision number, gene description, gene synonyms...it says "At the present time, it is possible to make annotation packages for the most common model organisms" I don't know how to proceed. Best regards Ingunn </div

Microarray Annotation GO Organism Microarray Annotation GO Organism

updated 16.2 years ago • Ingunn Berget

Entrez identifiers, mappings to GO, etc). I would be delighted to see support added for other organisms (especially for mouse) as Reactome database anyhow supports them. Any plans for that yet? - Asta</div

GO GO

updated 12.6 years ago • Asta Laiho

Hi, I am doing the RNA-Seq data analysis of a non-model organism these days, and a few questions occurred to me. The non-model organism doesn't have a orgDb, so I have to use the org.Hs.eg.db...of a GO term based on the human 'Background Gene Ratio' still meaningful for the non-model organism? Looking forward to your help

non-model enrichment organisms analysis

updated 3.2 years ago • yuhang

to use topgo for GO enrichment of RNA-seq data from tophat/cufflinks pipeline. I have a non-model organism and hence donot have GO mappings in bioconductor annotation package. How do I obtain the GO mappings for my organism

Annotation GO Organism topGO Annotation GO Organism topGO

updated 12.3 years ago • km

chapters from the Springer books, and I'm lost. I have a genome (and corresponding arrays) of an organism, along with GO assignments. I'd like to run an enrichment analysis. GOStats seems to need the db packages, is that correct

Organism GOstats Organism GOstats

updated 15.5 years ago • January Weiner

I found clusterprofiler neat and really want to give it a try. However, Im working on a non model organism and without kegg database annotation but with custom compiled kegg representatives for the model. Is it possible

clusterprofiler

updated 8.1 years ago • rozanskide

nbsp;How to pathway analysis of Arabidopsis thaliana organism using  pathview. Data  preparation for input and analysis

microarray pathview

updated 8.8 years ago • avinash gupta

all species, nor can I find a tool that can take an accession number and translate it into its organism's name. I am using R. Thank you for any help, J. Denton edit for clarification: for the accession number translation, an

AccNo OrgDb convert Organismname RStudio

updated 2.1 years ago • j_denton

NCBI database, for example, refseq\_rna? Similarly, I'd like to limit my search to a specific organism/taxid. ![https://screenshotscdn.firefoxusercontent.com/images/0d67820a-787a-4d5b-9eb0-1143113f4d20.png](https

blast blastsequences

updated 7.6 years ago • aush

Hey everyone, In order to do gene enrichment analysis on non-model organism (fungi), I obtained the KEGG ids using KOfam analysis. Using clusterProfiler enrichKEGG function I did the enrichment...t") colnames(file) <- c("ProteinID", "KO") file1<- (file$KO) kegg <- enrichKEGG( file1, organism = "ko", keyType = "kegg", pvalueCutoff = 0.05, pAdjustMeth…

clusterProfiler enrichment KEGG

updated 3.5 years ago • AP

I have whole genome seq data from a non-model organism (Bengalese finch - Lonchura striatta domestica), which I've mapped and annotated using another organism for which

DOSE hypeR goTools GOstats topGO

updated 5.0 years ago • Madza Farias-Virgens

I'm trying to create a custom database for Nothobranchius furzeri for use with my RNAseq data, but am having trouble. Any help will be appreciated. I downloaded the NCBI data manually and created the SQLite file by following the advice from James W. MacDonald (https://support.bioconductor.org/p/9152990/). ```r > writeFilesToDb <- function(file, file.dir = ".") { require("A…

AnnotationForge

updated 2.1 years ago • Adrian

Altman <naomi at="" stat.psu.edu=""> >Subject: Re: [BioC] which package can do GSEA for no model organism >Cc: >Bcc: >X-Eudora-Signature: <work> >Date: Mon, 29 Jun 2009 13:06:22 -0400 > >Dear Pengcheng, >You cannot really...gt; >Usually, we use a program such as BLAST to align the unigenes to the >nearest model orga…

GO Organism ASSIGN GO Organism ASSIGN

updated 16.4 years ago • Naomi Altman

version of SPIA (2.10.0) (available in the devel branch) that you can use to run SPIA on any organism available in KEGG starting with KEGG KGML files. It seems that there is a KEGGREST package from the bioc team that...Dan Tenenbaum showing how to get the files: library(KEGGREST) keggList("pathway") #or filter by organism (or T number): keggList("pathway", "hsa") keggGet("hsa05130", "kgml")…

Organism SPIA goseq KEGGREST Organism SPIA goseq KEGGREST

updated 12.8 years ago • Tarca, Adi

have a list of accession numbers from a proteomics experiment, and each number come from a different organism. For what I read until now, I found how to recover GO terms for organism specific databases as in: org.Mm.egGO[mappedLkeys...egids)] is there a way to do this for a diverse group of accession numbers from different organisms? Assuming that I have my list of annotated GO terms the most…

Proteomics GO Organism Proteomics GO Organism

updated 12.1 years ago • Ricardo Silva

Novartis data (Luscombe re-analysis E-TABM-145). This experiment contains samples from a number of organism parts. My aim is: 1. to compare the gene exprssions in a single organism part to the average expression in all samples

Organism BRAIN Organism BRAIN

updated 14.6 years ago • Hans

orgs <- subset(ah, ah$rdataclass == "OrgDb")</pre> This provides me with data from 1145 organisms, but missing are such important organisms as "Homo sapiens" and "Mus musculus". Why is this?  Thank you.  Eric &nbsp

annotationhub orgdb

updated 10.0 years ago • efoss

<div class="preformatted">Hi Iain, Yes, pathview can work with your problem. First map your genes to KEGG Orthology, and retrieve the KEGG ortholog IDs (gene IDs in the format of Kxxxxx) (as you have done). Just label your genes use these KEGG ortholog IDs (instead of Entrez Gene IDs or gene symbols). Then supply your data as gene.data, and set species="ko" when calling pathview function. O…

Pathways Organism pathview Pathways Organism pathview

updated 12.4 years ago • Luo Weijun

Is there any way to reduce the redundancy of a set of GO terms when working with a non-reference organism? I mean something similar to [REVIGO](http://revigo.irb.hr/). The problem with the last is that has a limit in the number...submitted. I have read the documentation of GoSemSim and it seems that can work only with supported organisms (though I expected that maybe it would have a function lik…

gosemsim go gene ontology

updated 10.6 years ago • cpcantalapiedra

When calling DESeqDataSetFromMatrix, should the design then include the main effects only (i.e. "~ organism + celltype") or should we also include the interaction effect (i.e. "~ organism + celltype + organism:celltype")? And when calling...function, how should we specify the interaction effect (I guess it should be something like c("organism:celltype", "human:celltypeX", "mouse:celltypeX"), wher…

deseq2 batch effect across species

updated 7.0 years ago • mjldehoon

div class="preformatted">Claire, You can try GAGE/Pathview for non-model organisms. They support ~3000 KEGG species. However, you need to have the full dataset instead of a pre-selected list of differentially...guest] wrote: Hello I would like to run an hypergeometric testing on KEGG terms for non- model organism. When it comes to Goterm I always use Gostats where I can enter my "universe" l…

Pathways GO Organism GOstats

updated 11.2 years ago • Luo Weijun

<div class="preformatted"> Hi all, I am currently trying to install an organism package built using the makeOrgPackageFromNCBI() function from the AnnotationForge Package. Unfortunately, when...div class="preformatted"> Hi all, I am currently trying to install an organism package built using the makeOrgPackageFromNCBI() function from the AnnotationForge Package. Unfortunately...to in…

Organism AnnotationDbi AnnotationForge Organism AnnotationDbi AnnotationForge

updated 11.8 years ago • Guest User

<div class="preformatted">Hello I would like to run an hypergeometric testing on KEGG terms for non- model organism. When it comes to Goterm I always use Gostats where I can enter my "universe" list and then my "target" genes and it works really well. However, when it comes to Kegg pathways, I tried to use go stats again but it's based on the kegg.db which is outdated and as a result I ge…

Pathways GO Organism GOstats

updated 11.2 years ago • Guest User

Hello, has anyone here ever done downstream analysis on differentially expressed genes in non-model organisms? I'm working with the axolotl, and I am wondering what tools and with which identifiers people would typically work

axolotl KEGG GOstats clusterProfiler

updated 2.4 years ago • georgii.vdovin

included in the package. Kindly guide me as to how to proceed with the transcriptome analysis of organisms not included here. Thank you Anuranjan

QuasR

updated 5.1 years ago • anuranjansrathore

at stat.math.ethz.ch >Asunto: RE: [BioC] Fwd: Re: which package can do GSEA for no model >organism >Fecha: Mon, 29 Jun 2009 13:06:40 -0400 > >> >>>To: Pengcheng Yang <yangpc at="" ioz.ac.cn=""> >>>From: Naomi Altman...naomi at="" stat.psu.edu=""> >>>Subject: Re: [BioC] which package …

Annotation GO Organism ASSIGN Annotation GO Organism ASSIGN

updated 16.4 years ago • Ana Conesa

library(GenomicFeatures) txdb <- makeTxDbFromGFF("/home/m.tub1.gff3",circ\_seqs=character(), organism="Mycobacterium tuberculosis") annoData <- genes(txdb) annoData1 <- as.data.frame(annoData) a <- annoData1\[which...lim\[1\], to = lim\[2\], type = "histogram") dev.off() Can Gviz handle any non-model organism by taking FASTA or any other method ? …

Gviz plot chipseq

updated 8.2 years ago • anupriyaverma1408

Dear All, How to create annotation package for not a supported (please see for available ones below) organism (e.g. D.magna: http://en.wikipedia.org/wiki/Daphnia_magna and other Crustaceans that are so important in environmental...As I know Biocore Data Team is responsible for the annotation packages. But how do the select organism to support? Thanks Alex References: http://www.bioconductor.…

Annotation GO Organism hgug4112a Annotation GO Organism hgug4112a

updated 14.2 years ago • Alogmail2@aol.com

Hi I am trying to build the organism package for sheep. At the first i used the codes that was in vignette help page. and so run makeOrgPackage.&nbsp

goseq

updated 7.4 years ago • Mehdi

div class="preformatted">Hi all, I would like to create the equivalent of org.Hs.eg.db for my organism of interest, Toxoplasma gondii. Could anyone point me toward the right direction. Is it just a query to NCBI with GeneID...This is to use the ChipPeakAnno package for ChIP-chip analysis of a non-mainstream organism. Do you think that is too much trouble, knowing it is not in Biomart? Thank…

Organism ChIPpeakAnno Organism ChIPpeakAnno

updated 14.6 years ago • Olivier Lucas

It would be great if the organism packages had a templated minimal vignette that included printing out the keytypes and columns. http://bioconductor.org

homo.sapiens organismdbi

updated 8.8 years ago • Michael Love

a blast of peptides obtained from a proteomics experiment, and each number come from a different organism. For what I read until now, I found how to recover GO terms for organism specific databases as in: org.Mm.egGO[mappedLkeys...egids)] is there a way to do this for a diverse group of accession numbers from different organisms? Assuming that I have my list of annotated GO terms the most sim…

GO Organism GO Organism

updated 12.1 years ago • Ricardo Silva

_organisms.pdf" and I´m trying now to use the enrichGO() function, which does not work with my organism yet.   The databases pointed out in the example: "bacteria\_mart\_14", "fungi\_mart\_13", "fungi" do not exist in listMarts

clusterProfiler go annotation

updated 10.5 years ago • cristina della beffa

div class="preformatted">Dear list, I work with a non-model organism (an ant) for which we sequenced the genome. The genome is on NCBI but isn't annotated in the standard R-accessible databases

Organism genomes Organism genomes

updated 13.2 years ago • Yannick Wurm

nbsp;        "supplementary_file"</code> Clearly, there should also be an "Organism" metadata field, e.g.: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4032 Clearly, there should also be an...Organism" metadata field, e.g.: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4032 Clearly, there should also be an "Organism...e.g.: https://www…

geometadb

updated 8.1 years ago • Bohdan Khomtchouk

pre> and I get this error message: <code>Error in .abbrevOrganismName(.getMetaDataValue(txdb, "Organism")) : <br/>   Organism should have a genus and species separated by a space,</code>   How could I get around this problem

makeTxDbPackageFromUCSC genomicfeatures

updated 8.8 years ago • Ugo Borello

should i use for the differential expression calculation and plotting? as the specie is not a model organism, how is it possible to do the gene ontology analysis and which package should i use to perform the gene ontology annotation

GO R RNAseq

updated 4.5 years ago • najib

from `` UCSC ``to form the anchor of the figure.  In case of  working with a non-model organism how to deal with this issue? Thanks a lot. D

omiccircos seganglepo sim.circos circos

updated 8.3 years ago • Didi

an old vignette on "How to use clusterProfiler to do GO enrichment analysis with unsupported organisms" I've got this error.  library(clusterProfiler) > Gff2GeneTable("all.gff3", compress=T) Reading all.gff3: found

clusterprofiler go Gff2GeneTable buildgo unsupported organisms

updated 9.0 years ago • Didi

Hi, I have a few questions about using goseq on a non-model organism: I have a set of DE-genes identified by DESeq2 called `` genes ``, a vector of gene lengths called `` lengthData `` created like

goseq go genesetenrichment

updated 10.0 years ago • Jon Bråte

help me to sovle the following problem? I only want to do gene enrichment analysis for a non-model organism and ppy_GOannot.txt acquired from http://www.ebi.ac.uk/QuickGO/GAnnotation. library("GOstats") library("GSEABase...4 GO:0005730 IEA A2BDH2 5 GO:0005783 IEA A2BDH2 6 GO:0005794 IEA A2BDH2 goFrome <- GOFrame(ppyGO,organism = "Pongo abelii") Error in .testGOFrame(x, organism) : inva…

GO Organism GO Organism

updated 12.3 years ago • Zhidong Yuan