Bioconductor Forum

to bioconductor and do not know much of the functionality. I came to know how to extract data for an organism, but don't know how to save it for to be used in mgoSim. any hints clues please. many thanks

AnnotationHubSoftware GOSemSim annotation

updated 3.9 years ago • Amandeep

Hello, I am trying to forge a genome for a non-model organism. I have generated the following seed file (in dcf format) and using the available Athaliana seed file as an example...as provided by NCBI (Bra_napus_v2.0, RefSeq assembly accession: GCF_000686985.2) Version: 1.0.0 organism: Brassica napus common_name: Rape genome: Bra_napus_v2.0 provider: NCBI release_date: 2017…

BSGenomeForge BSGenome

updated 4.7 years ago • sieminsk

I am working with a non model organism called Tenualosa ilisa. I am working with RNA-seq data. De novo assembly was performed using trinity. Foe kegg enrichment

RNAseq123

updated 3.0 years ago • afsanarupa1

For those that have added bioc-sync to a team within an organization in order to build a git-svn bridge, how long has it taken to get a response

git-svn bridge bioc-sync

updated 10.6 years ago • rcavalca

I wanted to use an organism org.Hs.eg.db package when using the function simLL as follows but it is not possible? <pre> >library("GOstats") &gt...I wanted to use an organism org.Hs.eg.db package when using the function simLL as follows but it is not possible? <pre> >library("GOstats") >library...a NA or something similar but not an error and a warnin…

gostats

updated 9.3 years ago • Lluís Revilla Sancho

circumventable by "download.file"s "wget" option. So I basically call "AnnBuilder:::getSrcUrl("all", <organism>)" to get the targets and then loop over them, retrieving the files, storing them locally and rewriting the srcUrl to...is wrong (?). Shouldn't that point at "ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current"? Cheers, Joh </organism></div

Annotation Annotation

updated 17.6 years ago • Johannes Graumann

about "evidence code" in data.frame from     GOstats packages with unsupported model organisms Message-ID: <50FED931.60706@fhcrc.org> Content-Type: text/plain Hi, The evidence codes are defined by the folks...a particular GO term to a specific gene ID.  For many genes to GO mappings in non- model organisms the association is "second hand", meani…

GO Organism GOstats GO Organism GOstats

updated 12.9 years ago • Fix Ace

Dear team of Bioconductor, The GO annotation of fungal species outside of 20 model organisms is outdated and a lot of genes miss GO annotation comparing to ensemble biomartr. ``` > bitr(x, 'SYMBOL', c("PMID", "GO", "ONTOLOGY...12 BCIN_01g09430 21876677 GO:0050525 MF ``` Could you please update the annotation of this organism in OrgDb at your earliest convenience? Thank you very m…

GO biomartr annotation ensemble fungi

updated 4.6 years ago • Bettina

bioconductor/attachments/20110308/92b2 7df4/attachment.pl ), except I am using a non-supported organism (Arabidopsis). I've come to the exact point in the analysis as Fernando has in the above link, where I would like to extract...the enriched GO terms in my DE analysis. My question is, how can I do this with a non-supported organism? For a supported organism, the process looks to be straight …

GO Organism PROcess goseq GO Organism PROcess goseq

updated 11.7 years ago • Dale Richardson

Hello everyone! To gain familiarity with enrichment analysis, I'm using a model organism to understand how the packages work. Then, I'll be able to conduct analyses on my non-model organism, which presents...PA1248, PA1875, PA5219, PA1076, PA0024)" > #KEGG analysis kk <- enrichKEGG(decs, organism="pae", pvalueCutoff=0.05, pAdjustMethod="BH", qvalueCutoff=0.1) --&…

enrichKEGG KEGGgraph KEGG

updated 21 months ago • cinzia.spagnoli

<div class="preformatted">Hi Iain, I am attaching the KO gene set data you need for your analysis. This data was generated the same way as gene set data in gage and gageData packages. For other users with similar needs, I will also provide this KO gene set data in the development version of pathview or gageData package soon. For your analysis, you may do something like: #load and check the…

Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO

updated 12.4 years ago • Luo Weijun

genome wide annotation package given one of the following or a combination of arguments to a script: Organism: Mmusculus Assembly: mm10 The result would be that the org.MM.eg.db package would be downloaded

annotationdbi organismdbi

updated 8.9 years ago • s1437643

the annotations of the specific species' Unigenes or other >> sequences from unsequenced organisms. The annotation contain user >> defined classes, such as GO, KEGG, IPR, etc. Once the packages/objects >> is created...gt; the >>>> >>>> >>>> >>>>…

Annotation GO Organism GOstats topGO ASSIGN Annotation GO Organism GOstats topGO ASSIGN

updated 16.4 years ago • Pengcheng Yang

differential analysis and am having trouble with adding annotation for GO using unsupported model organism (ie sheep, org.Oa.eg.db). Ovis aries (sheep) is not supported by "AnnotationForge" package, so I'm following the instructions...from "How To Use GOstats and Category to do Hypergeometric testing with unsupported model organisms by M. Carlson". I obtained the following error when I'm trying…

reportingtools annotationhub gostats

updated 9.4 years ago • cagenet34

Hi, I am trying to do GO enrichment analysis. I work on Cannabis sativa, which is a non-model organism. There are no GO terms for Cannabis, so I cannot make use of the orgdb or biomart functions in R. However, I have generated

clusterProfiler goseq topGO DESeq2

updated 3.5 years ago • Lucía

source of the function, it is set up to query human and mouse dbSNP data. Could it be that non-model organisms aren't supported for dbSNP reference data retrieval? Any help on this would be greatly appreciated. -Kristen

ensembl macaque dbsnp customprodb

updated 10.4 years ago • kristenbeck527

I am trying to run the GO enrichment analysis for a subset of genes from my non-model organism. And my gene IDs are look like :"gene1036:10" After creating a GOHyperGParams Object using the function GSEAGOHyperGParams...file, which is just a table with gene IDs and GO IDs. Do anyone know some tools for non-model organisms? Is it possible to run enrichment analysis based on a simple GO a…

gostats GO non_model

updated 7.6 years ago • zhaoran1124

nbsp; Some online search results suggest that I should install the annotation packages for the organism. But I seem to have trouble finding db packages for cat on bioconductor webpages. And the error message did not specify...I should install to solve the problem? And how to deal with this kind of situation (supported organism but difficult to find packages) in the future. Thanks in advance! &…

goseq genesetenrichment annotation

updated 10.3 years ago • xyliu00

lt;- "grey" names(label_color[label_color == "grey"]) <- "NA" names(label_color[label_color == "organe"]) <- "lysosome

EnhancedVolcano

updated 2.7 years ago • Phương Thùy

I have transcriptome data of an inhouse sequenced bacterial genome. I made the database for my bacteria using makeOrgPackageFromNCBI command. How can I use this database for KEGG AND Go analysis (ORA or GSEA). All commands use either KEGG organism database for such an analysis. I tried with that command (KEGGrich command) but it indicated that "Gene ids did not match...How can I use this datab…

clusterProfiler OrganismDb

updated 2.0 years ago • Aastha Kapoor

I run the command AnnotationForge from AnnotationForge package in r studio with the following inputs but I couldn't create my own custom database for Acinetobacter baumannii. I want to see gene set enrichment analysis from RNA-seq data with my mutated strain of Acinetobacter baumannii. This species is not available in r packages for GO analysis. first I ran the command with rebuildCache=TRUE …

AnnotationForge OrganismData OrganismDb

updated 2.4 years ago • abhisek001

Hi, I am analysing RNA Seq data on an organism that is not represented in the KEGG database. I have carried out differential expression analysis using deseq2

gage pathview KEGG Gene enrichment analysis

updated 6.1 years ago • MimR

Expected input gene ID: ND6,ND4,COX3,ND1,ND5,ATP6 --> return NULL...'. I am studying a non-model organism, the 'Vulpes lagopus'. My script is as follows, ``` mycounts<-read.csv("-B5_Counts-Arctic-fat.csv",row.names = 1) head(mycounts

organism non-model

updated 3.2 years ago • yuhang

div class="preformatted">I work with the plant Sorghum bicolor and want to make my own organism annotation package. I created package with makeOrgPackage and also tried the example in: http://www.bioconductor.org

GO

updated 11.2 years ago • Guest User

original REFSEQ id, but nothing has worked. Is there a specific package that works with non-model organisms that actually contains non-model species?  I have submitted some of my sequeces to Ghostkoala as a last ditch

rnaseq_analysis KEGG nonmodel species

updated 7.2 years ago • laural710

chrVII, "Scerevisiae_chr7.fasta", compress=FALSE)</pre> The problem is that I have many other organisms for which I must do the same. __OBJECTIVE__ How can I automate the export process in a way that the filename of the

bsgenome biocgenerics bsapply export

updated 7.8 years ago • ረ

hello, I am working on non model organism (aspergillus fungi) and I would like to perform the gene ontology analysis as well as KEGG pathway analysis. For gene...graphs? For the KEGG pathway analysis, which tool will be suitable for doing it for a non model organism? thank you for your help. Code should be placed in three backticks as shown below ``` #Note before analysis #make sure t…

GO KEGG TopGO

updated 4.4 years ago • najib

<div class="preformatted">Hi, I am using KEGGprofile to perform KEGG enrichment for a non model organism. Using the data from the R documentation i perfectely obtaine the enrichment. >data(pho_sites_count) >genes&lt...div class="preformatted">Hi, I am using KEGGprofile to perform KEGG enrichment for a non model organism. Using the data from the R documentation i perf…

KEGGprofile

updated 11.2 years ago • artur

<div class="preformatted">Dear Stefano, I've tested species Pseudovibrio FO-BEG1 ("psf" in KEGG database) and found it was imported into KEGG database in 2013 ( http://www.genome.jp/kegg-bin/show_organism?org=psf). But KEGG.db package was updated until 2012. I think that is the reason for the error message. Now I provide a new parameter "download_latest" in "find_enriched_pathway" function…

Organism KEGGprofile

updated 11.2 years ago • zhao shilin

chrominfo = chr.info, dataSource="gtf file for Arabidopsis lyrata", organism="Arabidopsis lyrata") Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame...Supporting package: GenomicFeatures # Data source: gtf file for Arabidopsis lyrata # Organism: Arabidopsis lyrata …

GenomicFeatures rtracklayer

updated 6.6 years ago • stephane.plaisance

GO annotations I'm retrieving from the hyperGTest and how they relate to the GO annotations in my organism's (saccharomyces cerevisiae) annotation database. In particular: for some enriched GO term X, I'm finding genes listed

Annotation GO Cancer GOstats Annotation GO Cancer GOstats

updated 15.3 years ago • Steve Lianoglou

<div class="preformatted">Dear All, Sorry for the late reply. I went underground for a bit. Thanks Marc, i did try the cdf option since affymetrix did provide a .cdf file for rice. I was however unable to annotate for gene names etc for the probe IDs using the cdf environment in the way i would do using any .db package. Maybe i am missing something but there must be a way to get this annota…

Microarray Annotation Organism cdf db0 probe annotate affy Microarray Annotation cdf

updated 12.6 years ago • Ekta Jain

afterwards expect to have "human", "mouse" or "rat" as the organism. Using debug(resourcerer2BioC) and setting organism back to "human" in the browser solves the problem. The first 2 lines...of resourcerer2BioC: { organism <- match.arg(organism) switch(toupper(organism), HUMAN = organism <- "Homo sapiens", MOUSE = organism <- "Mus musculus", RAT...organism =…

Organism Resourcerer Organism Resourcerer

updated 21.0 years ago • Francois Pepin

Hello- I am working with a non-model organism (_Bombus impatiens_) for which NCBI has some information (taxon id = "132113"), but no GO information. I learned this trying

AnnotationForge annotationforge nonmodel rnaseq

updated 8.0 years ago • mlpimsler

I am analysing differentially expressed genes in different immune cell types coming from different organs. I want to compare cell types within organs and also between organs (same type in different organs). I expect there are...in the gene expression among cell types. So, in order to analyse cell types within the same organ - let's say B Cells vs T Cells in the spleen - should I subset the dat…

DESeq2 RNASeq

updated 2.8 years ago • andrebolerbarros

if anybody can clarify, what the results output mean as it is concerning me slightly. I have 10 organs and 4 time points. I want to look for changes across time in general. I don't want an interaction term as I am only interested...change across time, and thats it. I will do gene patterns later on to look for similarities between organs etc... My question is, is the LRT test calculating changes …

DESeq2 LRT multiple time points

updated 7.8 years ago • A

KEGG). I face a problem right I try to create gseKEGG object. In the instructions there is said "organism KEGG Organism Code: The full list is here: https://www.genome.jp/kegg/catalog/org_list.html (need the **3 letter code...My problem is that my organism has four letter code "pfre" (Propionibacterium freudenreichii subsp. freudenreichii DSM 20271). Is there anything...what I could do to h…

clusterProfiler KEGGGeneSetEnrichmentAnalysis

updated 4.8 years ago • iidaL

wait for a fix on their behalf. In the meantime, we have shared some FELLA databases for common organisms [here][1]. [1]: http://b2slab.upc.edu/team/sergi-picart/ You just need to download the database of your organism of choice...FELLAdata)) # ... and resume your analysis We hope this helps, and apologise if your organism is missing in our list. EDIT1: KEGGREST is now …

FELLA software error

updated 6.1 years ago • sergi.picart

of RNA-seq data which I have combined with the first batch. Within both batches I have the same organ but different biological replicates... for example, 2 replicates of the lungs in batch 1 and 2 and the third and fourth...metadata sheet, all samples model well with DESeq2 with regards to replicates etc... apart from one organ.. the small intestine. The small intestine is actually recognised as …

deseq2

updated 7.2 years ago • A

require("affy") || stop("cannot load applera without affy") setClass("applera", representation(Organism="character", Geneid="character", Signal="exprSet", Sdev="exprSet", Cv="exprSet", Sn="exprSet", Flags="exprSet", Ctrl="list"), contains...exprSet", where=where) #Organism slot if(is.null(getGeneric("organism"))) setGeneric("organism", function(object) standardGeneric("organism")) setMethod...org…

applera applera

updated 20.3 years ago • raffaele calogero

I'm interested to look at the effects of treatment(infection) on the gene expression in each organ over time. I'm having troubles understanding how to define the reduced model to run DESeq. here is my code: ``` dds <- nbinomLRT...dds, full = ~Treatment + Organ + Time + Treatment:Time + Organ:Time, reduced = ~Treatment + Organ + Treatment:Time) #rlog transformation rld <- rlog(…

DESeq2

updated 3.4 years ago • Alex

  I am trying to build the goseq db for Mycoplasma hyorhinis.  Here is what I used: makeOrgPackageFromNCBI(version = "0.0.1", author = "me", maintainer = "me <me@mine.org>", outputDir = ".", tax\_id = "1129369", genus = "Mycoplasma", species = "hyorhinis", NCBIFilesDir = "."), but I find the error has following, could you please help me?? Gettin…

AnnotationForge

updated 10.0 years ago • songeric1107

I am trying to make db for Mycoplasma genus = "Mycoplasma", species = "hyorhinis", but I get error, could you please help. makeOrgPackageFromNCBI(version = "0.0.1", author = "me", maintainer = "me <me@mine.org>", outputDir = ".", tax\_id = "1129369", genus = "Mycoplasma", species = "hyorhinis", NCBIFilesDir = ".")   cache will try to rebuild once per day. Getti…

go

updated 10.0 years ago • songeric1107

to ask for your opinions on the following: I have 60 expression profiles of 60 samples (cells and organs in resting conditions). I normalized these arrays in many ways, including RMA. Considering the biological arguments...cells samples vs organs samples), I am planning to do the normalization separately, on the group of cell samples, and on the group of organ samples...My questions are: - aft…

Normalization GO gcrma Normalization GO gcrma

updated 18.1 years ago • Bogdan

dds<-DESeqDataSetFromMatrix(countData = countdata, colData = sampledata, design = ~ Time\_point + Organ) dds1 <- DESeq(dds, reduced = Organ, test = "LRT")... I am now getting this error: Error in DESeq(ddsAMIR, reduced = Organ, test = "LRT") :&nbsp...nbsp; object 'Organ' not found This is really confusing as the first function (DESeqDataSetFromMatrix works absolutely fine and…

deseq2 LRT reduced model

updated 7.8 years ago • A

Hi! I am trying to use makeOrgPackageFromNCBI() to build my own organism annotation package for Acinetobacter baumannii ACICU (taxid: 405416), but I got the following error "Error in prepareDataFromNCBI...Hi! I am trying to use makeOrgPackageFromNCBI() to build my own organism annotation package for Acinetobacter baumannii ACICU (taxid: 405416), but I got the following error "…

makeOrgPackageFromNCBI

updated 2.8 years ago • irene.artuso

oriza sativa - >osa). There is KEGG's pathway data for rice, but rice is not among those >organism in the extData directory of the SPIA package. Does anyone has >created their own pathway data to give it as input...KEGG data on which SPIA runs is provided in the SPIA's /extdata folder only for a few (most popular) organisms. The package size was the reason why I do not prov…

Organism KEGGgraph SPIA Organism KEGGgraph SPIA

updated 15.0 years ago • Tarca, Adi

from other organisms Populating gene2accession table: table gene2accession filled Getting data for gene2refseq.gz discarding...data from other organisms Populating gene2refseq table: table gene2refseq filled Getting data for gene2unigene discarding data from...other organisms Populating gene2unigene table: table gene2unigene filled Getting data for gene_info.gz discarding data from...…

makeorgpackagefromNCBI s.pombe sqliteExecStatement

updated 11.1 years ago • Parham

liver and the spleen, using 200 F2 mice. We thus need to measure gene expression levels in the two organs of 200 mice. We are using Agilent 4x44K arrays. For cost reasons, I was planning to label liver mRNAs with Cy3 and spleen...the same mouse on one array, and analyse liver and spleen data separately (eQTLs can differ in both organs). Of course, we expect gene expression variability between F2 …

updated 17.9 years ago • Marie-Paule Roth

where the problem could be. This is the relevant code: ```r ORA_GO <- function(gene_list, organism, ontology, pvalue) { # Select organism organism <- switch (organism, human = "Hsa", mouse = "Mmu" ) # Read annotation term2gene &lt...BP" = { annotation_file <- paste0("..…

clusterProfiler

updated 11 months ago • Fran

once! Is that really what you want? 4: In easyRNASeq(system.file("data", package = "RnaSeqTutorial"), organism = "Osativa", : You enforce UCSC chromosome conventions, however the provided annotation is not compliant. Correcting...genomicAnnotation(obj)), organismName(obj), : No function implemented to convert the names for the organism: Osativa. Available ones so far exists for: Dmelanogaste…

Annotation convert Annotation convert

updated 12.0 years ago • Guest User

I created and tested two Annotation Packages for two organisms, 1- **ORGANISM**: Galleria Galleriamellonella SPECIES: Galleria Galleriamellonella CENTRALID: GID Taxonomy ID: 7137...Db type: OrgDb Supporting package: AnnotationDbi 2-**ORGANISM**: Madurella Madurellamycetomatis SPECIES: Madurella Madurellamycetomatis CENTRALID: GID Taxonomy ID: 100…

OrgDb AnnotationDbi

updated 3.2 years ago • Imad

forgeBSgenomeDataPkgFromNCBI(assembly_accession="GCF_000001735.4", pkg_maintainer="Bruno Guillotin", organism="Arabidopsis thaliana", destdir=tempdir()) Warning in .extract_NCBI_assembly_info(assembly_accession, chrominfo...organism = organism, : "GCF_000001735.4" is a registered NCBI assembly for organism "Arabidopsis thaliana" --> ignoring supplied...organism' argument trying UR…

BSgenomeForge

updated 2.2 years ago • Bruno

Loading required package: RCurl Loading required package: bitops extracting only data for our organism from : gene2pubmed Getting data for gene2accession.gz extracting only data for our organism from : gene2accession...Getting data for gene2refseq.gz extracting only data for our organism from : gene2refseq Getting data for gene2unigene extracting only data for our organism from : gene2unig…

annotation annotationforge

updated 10.1 years ago • chiapello.m

some information, however, I found a little tricky problem-__No Uniprot information for some other organisms in AnnotationHub__, shown as below: For Homo sapiens: > library(AnnotationHub) > hub <- AnnotationHub() snapshotDate...unexpectedly, No "UNIPROT" in tomato! I think "UNIPROT" is one of the most basic information for any organism, it should be included. Therefo…

hub annotationhub

updated 4.9 years ago • wssdandan2009

<div class="preformatted">Hello, I've a question regarding the removeBatchEffect function in limma. I basically have a model expression_signal ~ organ + species + organ:species in which species can be considered a batch effect (I expect differences between species due to mainly due to array platform differences). I'd like to derive an expression signal matrix that's "corrected" for the spe…

limma limma

updated 12.4 years ago • arne.mueller@novartis.com

gene_info.gz > [5] gene2go.gz > getting data for gene2pubmed.gz > extracting data for our organism from : gene2pubmed getting data for > gene2accession.gz extracting data for our organism from : > gene2accession...getting data for gene2refseq.gz extracting data for our > organism from : gene2refseq getting data for gene_info.gz extracting > dat…

Bioconductor

updated 2.2 years ago • cinzia.spagnoli

performed to test the function. keggID <- c("K15179", "K03377") x <- enrichKEGG(keggID, organism='ko', keyType='kegg') --> No gene can be mapped.... --> Expected input gene ID: K10780,K16305,K08093,K14275,K18819,K22554 --> return...the example, ofc): Warning message: In bitr_kegg("K15179", fromType = "kegg", toType = "uniprot", organism = "hsa") : …

clusterprofiler

updated 6.6 years ago • jfo

Hello everybody, I have analysed my RNAseq dataset with RStudio and DESeq2. Now, I would like to use the output of DESeq2 to perform GO analysis. I am working with Verticillium dahlaie and I have understood that I have first to "make my organism package" using '''makeOrgPackageFromNCBI()'''. I have tried to run the code I found in the '''AnnotationForge''' vignette but, after extracting data …

AnnotationForge

updated 19 months ago • ussarizona

of microarray to color coded images. Specifically, the image is a line drawing of a plant with each organ coded with a unique color. The expression data correspond to different organs. I want to map these data to the corresponding...organs. The desired outcome is very similar to examples here: http://efp.ucr.edu/cgi-bin/absolute.cgi Based on my search, it seems

ggplot2 choropleth maps

updated 8.4 years ago • zhang.jianhai