Bioconductor Forum

affiliations, postal address, phone and fax numbers, and e-mail addresses of the workshop organizers (It is expected that organizers will be recognized experts in the related fields, and the organizing committee...and the capacity of the conference workshop program. Responsibilities of BIRD and of Workshop Organizers For all accepted proposals, BIRD will be responsible f…

PROcess PROcess

updated 18.0 years ago • Prof. Roland Wagner

encouraged. Workshops can vary in length, but most will be one full day in duration. Workshop organizers and attendees must register for their workshop and are permitted to join the main BIRD conference. *Requirements...affiliations, postal address, phone and fax numbers, and e-mail addresses of the workshop organizers (It is expected that organizers will be recognized experts in the…

PROcess PROcess

updated 18.1 years ago • Prof. Roland Wagner

AnnotationDbi") lines <- readLines(file) <span style="background-color:Yellow"> organism <- dbmeta(x, "ORGANISM") if(schema == "INPARANOID_DB" && organism != 'Homo sapiens'){ tableName <- sub(" ", "_", organism)</span> ii &lt

software error annotationdbi

updated 9.6 years ago • Burak Kutlu

bioconductor.org/packages/release/bioc/html/karyoploteR.html But, I am working with different organisms. I am able to find the organisms of interest using: > available.genomes() <code> [1] "BSgenome.Alyrata.JGI.v1"&nbsp...nbsp;   <br/>  [4] "BSgenome.Amellifera.UCSC.apiMel2.masked" </code>   My organisms of …

software error R bsgenome karyoploter

updated 8.1 years ago • kirannbishwa01

from 14 to 16 August 2009, in Tianjin, China. We cordially invite you to submit a paper(s) and/or organize an invited session. Due to numerous requests, the submission deadline is extended to 10 March 2009. Tianjin is one...sessions. The first author of each paper in an invited session must not be affiliated with an organization in China. All papers in the invited sessions will be marked as "Inv…

updated 16.8 years ago • ICNC'09-FSKD'09

from 14 to 16 August 2009, in Tianjin, China. We cordially invite you to submit a paper(s) and/or organize an invited session. Due to numerous requests, the submission deadline is extended to 10 March. Tianjin is one of the...sessions. The first author of each paper in an invited session must not be affiliated with an organization in China. All papers in the invited sessions will be marked as "I…

updated 16.8 years ago • ICNC'09-FSKD'09

<div class="preformatted">I use a lot of interaction data, assembled from hither and yon and usually on an ad hoc basis -- ranging from kinate-substrate relationships in yeast to human protein-protein interactions from pulldown experiments. Perhaps other do the same, which might mean there's a lot of duplicated effort in this area. I wonder: is there any bioc effort to collect, curate and …

updated 18.4 years ago • Paul Shannon

821280 5008021 830796</pre> <pre> > bitr_kegg(entrez_id, fromType='kegg', toType='uniprot', organism="ath") [1] kegg uniprot <0 行> (或0-长度的row.names) Warning message: In bitr_kegg(entrez_id, fromType = "kegg", toType = "uniprot...organism = "ath") : 100% of input gene IDs are fail to map... > bitr_kegg(entrez_id, fromType="ncbi-geneid", toTyp…

clusterprofiler

updated 8.8 years ago • chentong_biology

on March 8th)? Here is my conversion code: <pre> entrezgeneids = gsub('_at', '', row.names(expr)) organism = 'hsapiens_gene_ensembl' ensemble = useMart('ensembl'); hsp = useDataset(mart=ensemble,dataset=organism); ids = getBM(filters

biomart

updated 10.5 years ago • ebrudermanver

lt;- recount3::create_rse_manual( project = "SRP045225", project_home = "data_sources/sra", organism = "human", annotation = "gencode_v29", type = "gene" ) traceback() sessionInfo() ``` Unfortunately, I run into the following error...lt;- recount3::create_rse_manual( + project = "SRP045225", + project_home = "data_sources/sra", + organism = "human", + annotatio…

recount3

updated 18 months ago • PABLO ANTONIO

<div class="preformatted">Page 3 of the goseq documentation states "In order to link GO categories to genes, goseq uses the organism packages from Bioconductor. These packages are named org.<genome>.<id>.db, where <genome> is a short string identifying the genome and <id> is a short string identifying the gene identi_er. Currently, goseq will automatically retrieve …

GO Organism Apis mellifera goseq GO Organism Apis mellifera goseq

updated 13.8 years ago • Corby, Vanessa

I run makeOrgPackageFromNCBI to create annotation package. the following files are download: [1] gene2pubmed.gz [2] gene2accession.gz [3] gene2refseq.gz [4] gene_info.gz [5] gene2go.gz Code should be placed in three backticks as shown below ```r (((makeOrgPackageFromNCBI(version = "0.1", author = "Some One <so@someplace.org>", maintainer = "Some On…

AnnotationForge

updated 4.8 years ago • Imad

sessions. The first author of each paper in an invited session must not be affiliated with an organization in China. All papers in the invited sessions can be marked as "Invited Paper". One organizer for each invited session...with at least 6 registered papers will enjoy an honorarium of US*D 400. Invited session organizers will solicit submissions, conduct reviews and recommend accept/reject dec…

updated 16.1 years ago • ICNC'10-FSKD'10

connection, I get the error "Error in download.KEGG.Path(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... function (species) { keggpathid2extid.df <- kegg_link...pathway") if (is.null(keggpathid2extid.df)) stop("'species' should be one of organisms listed in 'http://www.genome.jp/keg…

Pathview Gene Mapping KEGG

updated 6.3 years ago • omarrafiqued

email = "michael.mozar@univ-perp.fr", biocViews = "AnnotationData", genomebuild = "Retroryza", organism = "Rice", species = "Oryza Sativa", url = "none") here my sessionInfo : library(pdInfoBuilder) ndf <- list.files(pattern = ".ndf", full.names...email = "michael.mozar@univ-perp.fr", biocViews = "AnnotationData", genomebuild = "Retroryza", organism = "Rice", species = "Oryza Sativa", u…

updated 14.6 years ago • Michael MOZAR

as follows: DESeqDataSetFromMatrix(countData = countdata, colData = sampledata, design = ~ Organ +Extraction+ Age ) DESeq(dds, reduced = ~Organ+Extraction, test = "LRT", parallel = TRUE) Extraction being the batch (for this run, only...two batches, 1 and 2). And i only want to see DE genes as a result of Age. Organ and batch (extraction) effects are therefore included in the red…

deseq2 batchcorrection

updated 6.2 years ago • A

for signature ‘"GRanges", "NULL"’</strong> In addition: Warning messages: 1: In supported_genesets()$organism == organism & genesets %in% supported_genesets()$geneset : longer object length is not a multiple of shorter object

chipenrich granges distancetonearest function dataframe

updated 8.1 years ago • rbronste

here, but instead to create my data object manually by specifying a two column data.frame and the organism in a separate slot. I'm however unsure how to do this. Is there a "quick" way to do this or should I look into R object oriented...5 PF01443 isogroup00001 6 PF01660 isogroup00001 > pfamFrame=KEGGFrame(pfamframedata, organism="XXXX") Error in .testKEGGFrame(x, organism) : None of el…

SNP Annotation GO Organism affy GOstats Category SNP Annotation GO Organism affy

updated 13.9 years ago • Henrik Hjarvard de Fine Licht

starting download for 5 data files 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 data for our organism from : gene\_inf…

bioconductor R annotationforge

updated 8.9 years ago • wssdandan2009

Hi Valerie, Thank you.Now I am able to use GOframe without any error. Initially I installed the ???AnnotationDbi??? and I assumed that ???biocLite("AnnotationDbi")??? will install the latest version. > source("http://bioconductor.org/biocLite.R") > biocLite("AnnotationDbi") BioC_mirror: http://bioconductor.org Using R version 2.15, BiocInstaller version 1.4.9. Installing package(s) 'Anno…

GO BiocInstaller GO BiocInstaller

updated 12.7 years ago • Guest User

Dear All, I have a non model reference genome which is not found in in public databases, as it is mentioned in GAGE vingnatte, I used the following commands to generate the KEGG gene set kg.ko=kegg.gsets("ko") kegg.gs=kg.ko$kg.sets\[kg.ko$sigmet.idx\] and found the following results, $\`ko00970 Aminoacyl-tRNA biosynthesis\` \[1\] "K00604" "K01042" "K01866" "K01867" "K01868" "K…

gage package gage

updated 7.4 years ago • melkile26

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20050819/ 4358def7/attachment.pl

updated 20.3 years ago • Bornman, Daniel M

Hi Wejun, I am new to BIOC and Pathview/Gage packages. I am analysing microarray data from an experiment on Atlantic salmon and I am attempting to visualize the results in Pathview, if possible. Following up a previous thread (https://stat.ethz.ch/pipermail/bioconductor/2013-August/054161.html), I have been trying to do a similar thing and I believe I have similar limitation. As for the previou…

Annotation pathview Annotation pathview

updated 12.2 years ago • Christian De Santis

of cybersecurity training in pune and offers comprehensive courses to equip individuals and organizations with the necessary skills and knowledge to safeguard against cyber threats. ![enter image description here...in their careers. WebAsha Technologies also offers corporate training programs tailored to an organization's specific needs and requirements. By enrolling in cybersecurity training in…

EDIRquery

updated 2.5 years ago • webasha23

ASBase, srcUrls =ASSrcUrls, baseMapType = ASBaseType, pk gName="Sigma Oligo 071205", pkgPath=ASDir, organism="Mus musculus", version="1.1 .0", author = list(author = "Anja E. Schiel", maintainer ="Anja E. Schiel<a.e.sc at="" hiel="" lumc.nl="">")) Attaching...package:AnnBuilder : GO Warning message: Built for UCSC is not valid! in: getUCSCBuilt(organism) Error in loadFromUrl(src…

Annotation GO AnnBuilder oligo Annotation GO AnnBuilder oligo

updated 20.0 years ago • A.E.Schiel@lumc.nl

Hi, I was wondering if it is possible to run DESeq ( or for that reason any other tool for differential expression analysis) to identify  significant differences between two organisms (for our research human and mouse). I know that we have two different sets of genes, but what if we can overcome this problem...tool for differential expression analysis) to identify  significant…

deseq2 cuffdiff differential gene expression

updated 10.4 years ago • Assa Yeroslaviz

create a list of all reactome pathway of the GO term analysis. ```r gsepa <- gsePathway(geneList, organism = "mouse", exponent = 1, minGSSize = 10, maxGSSize = 500, pvalueCutoff = "none", pAdjustMethod = "BH", verbose = TRUE, seed = FALSE) go.df...Description)) { GOList[[i]] <- viewPathw…

ReactomePA

updated 3.5 years ago • curiousmind007

environ" "ko" "genome" "compound" [10] "glycan" "reaction" "rclass" "enzyme" "organism" Note that: * `` vg ``, `` ag ``, `` dgroup ``, `` genes ``, `` ligand `` are available but not listed * `` organism `` is listed but not available The

KEGGREST bug

updated 8.3 years ago • olj23

that allows to perform enrichment in genomic regions from a list of genes, for non-human model organisms. Thanks

Enrichment clusterPro WGCNA

updated 3.4 years ago • María José

string that doesn't do anything in practice): ``` regulondb <- function(database_conn, organism, genome_version, database_version) { stopifnot(is(database_conn, "SQLiteConnection")) stopifnot(is(organism, "character...database_version, "character")) new( "regulondb", database_conn, organism = organism…

regutools

updated 3.4 years ago • a.giachino2

genomic.acgt = getBackgroundFrequencies(BSgenome.Athaliana.TAIR.TAIR9)<br/> Error in getPromoters(organism) : <br/>   Promoter sequences cannot be retrieved automatically for TAIR9, please provide a set of background...span>> Prom1000bp.genomic.acgt = getBackgroundFrequencies(Prom1000bp)<br/> Error in getPromoters(organism) : <br/> …

pwmenrich bsgenome

updated 10.3 years ago • oliwindram

wd\\V-eff\\GCA_007735645.1\\genomic.gff", format="auto",chrominfo=s, dataSource="GCA_007735645.1", organism="Venturia.effusa", taxonomyId=50376,dbxrefTag="GENEID") > tx TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures...Data source: GCA_007735645.1 # Organism: Venturia.effusa # Taxonomy ID: 50376 # miRBase build ID: NA # Genome: GCA_007735645.1 # Nb of tr…

OrgDb BSgenome

updated 2.1 years ago • mat149

<div class="preformatted"> I am interested in analysing the differential expression of the transcriptome of A.flavus grown at two different condition using easyRNASeq and DEGSeq. I have the raw reads in fastq format for the expt. I had mapped these reads to the reference genome sequence using bowtie and the output bam file was given as input to easyRNASeq. It gave the error ".doBasicCoun…

Annotation Organism DEGseq easyRNASeq Annotation Organism DEGseq easyRNASeq

updated 12.9 years ago • Guest User

<div class="preformatted">Hi, Lina, We are lucky in case of chicken. I just updated AnnBuilder (v1.11.7) to support Gallus gallus (taxon id 9031). You can get it from svn right away or wait 2 days to download it from bioc website. Or if you want to try it now, here is the changes: ================================================================ --- IPI.R (new) +++ IPI.R (old) …

Annotation Organism Gallus gallus probe AnnBuilder Annotation Organism Gallus gallus probe

updated 19.3 years ago • Nianhua Li

We have been interested in a range of topics related to the origins and evolution of vertebrate organs. In the framework of our research, we generate and analyze comprehensive genomics (e.g., RNA-seq, ATAC-seq) datasets based...on samples from our large organ collections. More recently, we have begun to bring the work of our lab to the level of single cells using state-of-the-art...Khaitovich, P.…

single-cell evolution Genomics Postdoc

updated 4.2 years ago • henrik.kaessmann

you in advance! Cheers Natalia here is my code: > count.table <- easyRNASeq("/RNAseqGallus", organism="Ggallus", chrSizes="chrSizes", annotationMethod="gtf", annotationFile="Gallus_gallus.Galgal4.73.gtf", count="genes...exon_number, gene_name. Adem??s: Mensajes de aviso perdidos 1: In easyRNASeq("/RNAseqGallus", organism = "Ggallus", chrSizes = "chrSizes", : Your organism has n…

Annotation Organism BSgenome BSgenome DESeq easyRNASeq Annotation Organism BSgenome DESeq

updated 12.1 years ago • Guest User

preformatted">Dear Bioconductor developers, Is Bioconductor software free for industry or profit organizations? Thanks, Fangyi </div

updated 23.2 years ago • luo.f@pg.com

on this page: https://learn.gencore.bio.nyu.edu/rna-seq-analysis/gene-set-enrichment-analysis/ ```r organism = "org.At.tair.db" BiocManager::install(organism, character.only = TRUE) library(organism, character.only = TRUE) sorted_dfx...800, pvalueCutoff = 0.05, verbose = TRUE, OrgDb = organism, by = "fgsea", pAdjustMethod = "no…

clusterProfiler enrichplot clusterpro doseR dose

updated 3.4 years ago • rama

I am creating a TxDb annotation package, and I have noticed that even if the organism information used to create the TxDb  contains more information than the species and genus, that will not be...24_PbergheiANKA.gff" txdb <- makeTxDbFromGFF( file = url, dataSource = "PlasmoDB 24", organism = "Plasmodium berghei ANKA", chrominfo = <chrominfo> …

genomicfeatures txdb

updated 10.6 years ago • Diego Diez

I was planning on using the Bioconductor package GOstats to identify these processes; however, the organism under study is not a supported organism. I have attempted to use the blast2GO software to generate the gene to GO mapping

Microarray GO Organism PROcess GOstats Microarray GO Organism PROcess GOstats

updated 11.8 years ago • Guest User

as provided by SGN (v3.0, 2017) and stored in Solanum lycopersicum genome browser Version: 3.00 organism: Solanum lycopersicum common_name: Tomato provider: SGN provider_version: SL3.00 release_date: Feb. 2017 release_name...SL3.00 source_url: https://solgenomics.net/organism/Solanum_lycopersicum/genome/ organism_biocview: Solanum_lycopersicum BSg…

BSGenome

updated 6.1 years ago • zen

as you can see down there....someone can help me? > pred.comp = gene2pathway.signaltrans("19713", organism = "hsa") Using KEGG information from SOAP service ... Mapping to signal transduction pathway components via KEGG database...found for 0 genes done. 1 genes to predict Retrieving information from InterPro database for organism ' hsa ' via Ensembl ... Checking attributes ... ok Check…

Organism gene2pathway Organism gene2pathway

updated 15.7 years ago • Alberto Goldoni

manually look up all the ~14000 references I have in total. Some of these references are from other organisms, like studies in tomatoes or humans. Using the original citation, I could search in literature databases (via {fulltext...tidypmc} or {europepmc}) and try to find which of them are from microorganisms (scanning for organisms names retrieved via {taxadb}). But I would want to avoid dev…

brendaDb

updated 3.4 years ago • Lluís Revilla Sancho

Hi, I was exploring the rhesus macaque package: > TxDb.Mmulatta.UCSC.rheMac8.refGene TxDb object: \# Db type: TxDb \# Supporting package: GenomicFeatures \# Data source: UCSC rheMac8 refGene \# Organism: Macaca mulatta \# Taxonomy ID: 9544 \# miRBase build ID: NA \# Genome: NA \# transcript\_nrow: 6378 \# exon\_nrow: 46356 \# cds\_nrow: 43281...Db type: T…

txdb TxDb.Mmulatta.UCSC.rheMac8.refGene

updated 7.4 years ago • Brian Smith

<div class="preformatted">Dear Nico, I've read a number of posts in different forums (including BioC) from people desiring to adapt annotations in order to deal with overlapping synthetic exons. You indicated in this forum (Wed Jan 9, 2013) that you were working on an example, in the easyRNASeq developer version, on how to perform this type of adaptation of an annotation. Similarly, I wou…

Annotation Organism easyRNASeq Annotation Organism easyRNASeq

updated 12.8 years ago • Bayles, Darrell

Hi, I am working on a non-model organism that I can't download the annotation package from the annotationhub. So I need to build an orgDb from scratch in order...to perform the GO enrichment analysis. For this organism, I already have the mapping of the gene ID (internal) to the GO ID. So I used the R package called "AnnotationForge" to build...I followed this example to built: * lib…

clusterprofiler

updated 4.7 years ago • zengjia0808

Hi there! I would like to perform KEGG enrichment with some differentially expressed gene data from RNAseq data. I am working on a non-model organism. I have 1) KEGG to GeneName Mapping ``` head(expr5_FS_final) KEGG unigene_FS 1 K02727 FS_gene_1 2 K17277 FS_gene_3 3 K17307...with some differentially expressed gene data from RNAseq data. I am working on a non-model organism. I …

KEGG clusterProfiler

updated 2.8 years ago • ruiqi.li

OK Checking exons...OK Warning message: In ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = organism, : I'm missing column(s): 'entrezid'. The corresponding database column(s) will be empty!</pre> Can anyone assist me

ensembldb

updated 9.6 years ago • stianlagstad

and with the 'term' and 'ontology'. Goseq just report the totals (ej: 800 genes are 'BP' and 'single-organism cellular process'). In other words I want to answer the question: which prunus persica genes are part of the term 'single...organism cellular process' under the ontology 'Biological Process'?. Thanks in advance

r goseq go

updated 9.4 years ago • tobal.92

hsa03440.xml hsa03450.xml,hsa04520.xml in the SPIA hsaSPIA.RData file? makeSPIAdata(kgml.path=mydir,organism="hsa",out.path="./") [1] TRUE But if I run spia(de=diff_exp,all=all_exp,organism="hsa",data.dir="./",nB=2000,plot s=FALSE,beta=NULL,combine

Pathways SPIA Pathways SPIA

updated 11.8 years ago • Guest User

myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "agilentOligo", pkgPath = myDir, organism = "Mus musculus", version = "1.1.0", author = list(author = "sylvain", maintainer = "sylvain at sdsc.edu"), fromWeb = TRUE) Error in "[.data.frame...columns selected In addition: Warning message: Built for UCSC is not valid! in: getUCSCBuilt(organism) > sessionInfo() R version 2.2.0…

GO Organism annotate AnnBuilder GO Organism annotate AnnBuilder

updated 19.9 years ago • Sylvain Pradervand

<div class="preformatted">I'm trying to calculate gene similarities for the yeast organism, but no matter which ontology or which term similarity I employ I get a lot of zeros in the gene similarity matrix. In...div class="preformatted">I'm trying to calculate gene similarities for the yeast organism, but no matter which ontology or which term similarity I employ I get a lot of zeros in …

Yeast Organism GOSim Yeast Organism GOSim

updated 13.2 years ago • Pablo Andretta Jaskowiak

GO/KEEG enritchment for non-model bacteria - help for beginner Hi everyone, I just begin with my RNAseq analysis and I am on the last step My organism is a new strain of Aminobacter genus, closely related to Aminobacter aminovorans KTC2477 (KEEG entry T04342, aak 83263). In fact is the same specie but, in contrast with the reference specie, my strain won an symbiotic island from other organ…

bacteria GO KEEG RNAseq

updated 5.6 years ago • liz.marjory

features to a BSgenome package or a txdb package in case there isn't an orgDB package for non model organisms? Is it easy to do it? Thanks a lot.  Regards, D

bsgenome txdb annotation orgdb

updated 8.4 years ago • Didi

similar to what Blast2GO does. Are there any packages that can do this? I am working on a non-model organism. Jon

GO BLAST annotation

updated 11.2 years ago • Jon Bråte

gt; genomic.acgt = getBackgroundFrequencies("BSgenome.Mmusculus.UCSC.mm10") Error in pickGenome(organism) : Please pick one of the valid organisms: "dm3" or provide a BSgenome object of the target genome. I would appreciate any

BSgenome convert BSgenome PWMEnrich MotifDb

updated 11.3 years ago • deepti anand

data file for all 483 xml files for the KEGG Orthology (KO) Database. I'm working with a non-model organism that is not supported by KEGG as it's own organism, so I have to use the [KEGG Orthology][1] (KO) Database instead of a 3-letter...code for an organism. I am running into an array out of bounds error and I was hoping that I could get help figuring out this issue. Is this...SPIA documentati…

SPIA

updated 2.1 years ago • Benji Bromberg

analyzed comprehensive genomics (e.g., RNA-seq, ATAC-seq) datasets based on samples from our large organ collections. More recently, we have begun to bring the work of our lab to the level of single cells using state-of-the-art...Khaitovich, P., Cardoso-Moreira, M., and Kaessmann, H. (2021) Alternative splicing during mammalian organ development. Nat. Genet. 53:924-935. Wang, Z.Y., Leushkin, E…

PhD single-cell ComparativeGenomics evolution

updated 4.2 years ago • henrik.kaessmann

Hi, I am writing because I am using UniProt.ws package for proteome retrieval. I'm trying to do this by giving as input the taxon ID for a certain organism. So I get the IDs with keys() and then I use select() to retrieve the information I need from each ID. The problem is if I try downloading the human proteome, the select() part is really time consuming. As an example: ```r library(U…

UniProt.ws UniProt

updated 5.0 years ago • JavierM

of pathways IDs (PATHID column). Before there was 20800 pathways with pathways beeing specific to an organism. Now there are 2185 pathways, shared between organisms. I'm not sure what were the reasons for the change, but I don't have...fgsea) and I need to fix it, I wonder is this transition final? If yes, may be it's better to remove organism specific prefix whatsoever? I'm pretty sure it's much…

reactome.db fgsea

updated 8.6 years ago • assaron