Bioconductor Forum

Warning message: no not accessible  I was wondering whether there is a specifically way to organize the bam file which could be read in the dba project.  Thank you so much.       &nbsp

edger

updated 10.7 years ago • yijing.su

Hi All, Could anyone please elucidate advantages of having an Annotation package for an organism or point me to any documentation that clearly lists all the various thoughts behind coming up with an Annotation

Annotation GO Organism Annotation GO Organism

updated 12.6 years ago • Rameswara Sashi Kiran Challa

i did not find genesets my organism of interest in the search page of GSEA: http://www.gsea-msigdb.org/gsea/msigdb/search.jsp Can I use the pathawy genesets

pathway KEGGREST GSEA

updated 4.7 years ago • MOHAMMAD

Hi there. I am trying to find a way to get a specific list of the additional parameters that are specified within the `...` argument of a function inside a library. How do you do that? In particular I would like to know the parameters accepted by the function `viewPathway` inside the ReactomePA package. By typing `formals(viewPathway)` I get: $pathName $organism [1] …

ReactomePA clusterProfiler

updated 5.8 years ago • lucap

sequence.gff3") ``` which yields the error message: ``` Error in .checkExtractVersions(gff, organism, genomeVersion, version) : The file name does not match the expected naming scheme of Ensembl files ( <organism>.<genome...version="">.<ensembl version="">) hence I cannot extract any information from it! Parameters 'organism', 'genomeVersion' and 'version' are thus required!…

ensembldb RNASeq

updated 4.7 years ago • Torkel

id format ids<-bitr(names(original_gene_list), fromType = "ENSEMBL", toType = "ENTREZID", OrgDb=organism) dedup_ids = ids[!duplicated(ids[c("ENSEMBL")]),] df2 = g[g$gene_id %in% dedup_ids$ENSEMBL,] df2$Y = dedup_ids$ENTREZID # Create a vector...decreasing = TRUE) ``` ```{r} kegg_organism = "mmu" kk2 <- gseKEGG(geneList = kegg_gene_list, organism = kegg_organi…

RNASeqR GO clusterProfiler rnaseq KEGG

updated 4.2 years ago • ICELANDICWATER

<div class="preformatted">Dear all, I have noticed that BSgenome.Mmusculus.UCSC.mm10 does not contain entries for upstream sequences (upstream1000, upstream2000, upstream5000) like for example BSgenome.Mmusculus.UCSC.mm9 does (see bellow). Is there a reason for this? Thank you, Diego > library(BSgenome.Mmusculus.UCSC.mm9) > Mmusculus Mouse genome | | organism: Mus musculus …

Mus musculus BSgenome BSgenome Mus musculus BSgenome BSgenome

updated 12.1 years ago • Diego Diez

c. homology package now maps internal HomoloGeneIds to homoData objects that has slots for organism name, LocusLink ids, internal HomoloGeneIds, GenBack Accession numbers, type of similarities, percent of identity...and urls for homologous genes in other organism. Environment LL2HGID maps LocusLink ids to internal HomoloGeneIds. d. New annotation data…

Annotation GO Organism hgu95av2 mguatlas5k mgug4121a rgug4130a probe Category Annotation

updated 21.6 years ago • John Zhang

etc. at the conference website: http://www.camda.info We look forward to a lively contest! The organizers and chairs of CAMDA 2013 Chairs: Joaquin Dopazo, CIPF, Spain Sepp Hochreiter, Johannes Kepler University, Austria...David Kreil, Boku University, Austria Simon Lin, Marshfield Clinic, U.S.A. Local organizer: Djork-Arné Clevert, Johannes Kepler University, Austria Contact: camda@bioinf.jk…

Sequencing Microarray Genetics Classification Clustering Regression Sequencing Microarray

updated 12.7 years ago • CAMDA 2013

<div class="preformatted">hi all, I try to use ABPkgBuilder (session info below) with following code (partly from the vignette) ##### library(AnnBuilder) read.table(file.path(.path.package("AnnBuilder"), "data", "thgu95a"), sep = "\t", header = FALSE, as.is = TRUE) myBase <- file.path(.path.package("AnnBuilder"), "data", "thgu95a") myBaseType <- "gb" myDir <…

Annotation GO Organism annotate AnnBuilder Annotation GO Organism annotate AnnBuilder

updated 18.2 years ago • Matthias E. Futschik

wrong? My script at least: library(KEGGgraph) tmp <- tempfile() retrieveKGML("00900", organism="csav", destfile=tmp, method="auto", quiet=TRUE) mapkKGML <- system.file("extdata", "csav00900.xml", package = "KEGGgraph") mapkG

KEGGREST GenomicDistributionsData KEGGgraph KEGG

updated 20 months ago • fernanda.backsouza

Suppose on NCBI BLAST website I insert one query sequence and hit BLAST with Homo sapiens as organisms. I extract the description of the first hit and paste it aside the sequence in the excel sheet (same round different

SequenceMatching SequenceAnnotation

updated 3.7 years ago • Prateek

www.ensembl.org"), 10) ###marts providing annotation for specific classes of organisms### head(biomaRt::listDatasets(biomaRt::useMart("ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org")), 100

biomaRt DESeq2

updated 4.1 years ago • adeler001

I now have an expression profile of an organ at various developmental time periods, such as 3 replicates in the first week, 5 replicates in the second week, 4 replicates

tissueTreg

updated 2.8 years ago • guang-hui

Warning message: In file(con, "r") : cannot open URL 'http://www.UniProt.org/UniProt/?query=organism:9606&format=tab&columns=id': HTTP status was '301 Moved Permanently'.</pre> Even after setting internet to true

bioconductor uniprot.ws

updated 10.0 years ago • beingseema03

preformatted">Can anyone direct me to an example of using hyperGTest with a KEGGHyperGParams? My organism is yeast and -- since my experimental data is from proteomics -- I have been happy using the YEAST annotation package

Annotation Yeast Organism Annotation Yeast Organism

updated 18.2 years ago • Paul Shannon

div class="preformatted">HI all, I have paired-end RNAdata from five different tissues of the same organism, I calculated the read counts using HTSeq tools and now I want to see which are the transcripts which are differentially

updated 13.3 years ago • Srikanth Manda Srinivas

the entrez ID and the logfoldchange in it. Error in spia(de = DE\_Colorectal, all = ALL\_Colorectal, organism = "hsa",  :   de must be a vector of log2 fold changes. The names of de should be included in the refference array! &nbsp

SPIA

updated 9.5 years ago • saamar.rajput

ENSG00000174871","ENSG00000112531") GOsim\_matrix <- mgeneSim(genes=mytestgenes,ont="MF",organism="human",measure="Wang",verbose=T) I am assuming that GOsemsim only works with enrez ids and I was wondering if there is

Ensembl GOsemsim GO semantic similarity

updated 9.3 years ago • saadmurtazakhan

researchers who use Bioconductor packages regularly. Pseudomonas aeruginosa is not one of the 20 organisms currently incorporated in OrgDb, but it looks as though many tools exist to construct a properly formatted database

OrgDb

updated 4.7 years ago • Thomas.H.Hampton

Can anyone explain the "CalcNormFactors" normalization process in edge r?  I have RNAseq data from insect antennae. I do not have a genome assembly for my organism, but I did assemble the transcriptome using trinity. I then retrieved my transcripts of interest (chemosensory genes...in edge r?  I have RNAseq data from insect antennae. I do not have a genome assembly for my organi…

edger

updated 7.0 years ago • phickner2

I am new regarding the KEGG pathway enrichment analysis. I have an in-house assembled genome and used it for RNAseq analysis. I did KEGG annotation using GhostKOALA and then used the KO annotation for GSEA analysis using ClusterProfiler (version 4.4.4). It ran smoothly but the enrichment result was a list of KO entries. I guess it makes sense since I used this KO annotation as the TERM2GENE input…

clusterProfiler

updated 3.1 years ago • Susanne

Hello, I have been pointed out [here](https://support.bioconductor.org/p/100092/#100095) that is possible to use [limma](https://support.bioconductor.org/p/76482/) to do any analysis, including KEGG or GO analyses of a new species. How is it possible to create an annotation database using annotationHub() or by supplying the gene.pathway data.frame directly for my non-model species? Thank you i…

limma kegg topgo dataframe edger

updated 8.3 years ago • mictadlo

Hi, I'm running a WGCNA analysis to detect correlating genes between a Virus and a host. My issue here is, that, over the course of the infection, the relative amount of host transcripts is decreasing from 100% to around 20%, so by normalizing over host and virus transcripts together, all finer differential dynamics are overshadowed by this trend. For a DE-analysis with DESeq2, I run the whole a…

RNA-Seq DESeq2 WGCNA Normalization

updated 4.9 years ago • wrzl

Loading required package: RCurl Loading required package: bitops discarding data from other organisms Populating gene2pubmed table: table gene2pubmed filled Getting data for gene2accession.gz discarding data...data from other organisms Populating gene2refseq table: table gene2refseq filled Getting data for gene2unigene discarding data from...other organisms Populating gene2unigene table: table ge…

Annotation GO db0 PROcess Annotation GO db0 PROcess

updated 12.3 years ago • Guido Hooiveld

Dear Marc and Hervé, I believe the AnnotationForge package is currently not working correctly. Perhaps due to an update in SQL functions? To keep it as simple as possible, I simply tried to reproduce the worked example in Marc's "Making Organism packages" vignette. It required one small modification on the last line to run (type="source"), so I'll paste in the whole code here: ``` library(…

AnnotationForge Marc Carlson Hervé Pagès

updated 5.7 years ago • Cei

two conditions (control and mutant) using S.pombe as a spike-in (because the antibody works in both organisms). The reason because we add spike-in is that the antibody is not very efficient so we wanted to normalise the immunoprecipitation

ChIPSeq SpikeIn edgeR Normalization

updated 4.4 years ago • maria.soler

for rice (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 to

SPIA SPIA

updated 15.1 years ago • Lourdes Peña Castillo

there will be a Bioconductor Developers' Meeting on 4.+5. April 2007 in Lausanne, Switzerland. Local organizer is Darlene Goldstein and the Vital IT centre. Mark your calendars. Details of the programme will be announced soon

Biobase Biobase

updated 19.0 years ago • Wolfgang Huber

<div class="preformatted">I have a use case that I am not sure the best way to proceed. I have a non-model organism for which we would like to know the sequence for a set of genes. It's a bird species, and I can for example align to the zebra...preformatted">I have a use case that I am not sure the best way to proceed. I have a non-model organism for which we would like to know the seq…

Organism

updated 11.3 years ago • James W. MacDonald

When I used the demo sqlite file, there are some outputs ```r >sqlfile_demo <- getSQLiteFile(destdir = "~/bin/Rpack", destfile = "GEOmetadb.sqlite_demo.gz",type="demo") >con <- dbConnect(SQLite(),sqlfile_demo) >getBiocPlatformMap(con)[1:5,] title gpl bioc_package…

GEOmetadb GEOmetadb.sqlite dbConnect

updated 2.2 years ago • Lee

<div class="preformatted">As low as 0.5 for pearson and 0.8 for spearman But I'm not holding up my data as a shining example Surely if there is a lot of natural variation in the biological system, then you're going to get large variation between biological replicates. -----Original Message----- From: Naomi Altman [mailto:naomi@stat.psu.edu] Sent: 28 February 2004 05:20 To: michael watson (…

Microarray Microarray

updated 21.8 years ago • michael watson IAH-C

http:> > > Are you asking about creating a snp annotation package for a different > organism? > > Yes how do I include snp annotation package of a different organism ? Thanks kmo > > > > On 11/26/11 11:03, km wrote

SNP Annotation Organism Homo sapiens BSgenome SNPlocs BSgenome SNP Annotation Organism

updated 14.0 years ago • km

and standards setters (and wannabes), brought together in in one 3 ring circus by the O'Reilly organization, the people who document Open (and some closed) Source IT with their retro-animal covered screeds on Perl, Python...I did attend the 2002 conference, liked most things, didn't like some things, then got hit up by the organizers, to assure more-of-the-former/less-of-the-latter and so have be…

updated 23.0 years ago • Harry Mangalam

<div class="preformatted">Hi, I am trying to build an annotation package starting from Applera Mm array, but I got this strange error running ABPkgBuilder Error in "parser<-"(`*tmp*`, value = "/usr/lib/R/library/AnnBuilder/scripts/llParser4LL") : No direct or inherited method for function "parser<-" for this call Any suggestion? Raffaele (Fedora core 2, R 2.0.0, Bio…

Annotation GO Organism applera Annotation GO Organism applera

updated 20.8 years ago • raffaele calogero

<div class="preformatted">Hi everyone, I'm trying to rebuild my annotation package for an Agilent chip using Resourcerer and it's not finder one of the parsers. The basic error is: >resourcerer2BioC("Agilent_HumanGenome.zip", organism="human") Warning: cannot open file `NA' Warning in unifyMappings(base, eg, ug, otherSrc) : Failed to get or parse Entrez Gene data because …

Annotation Organism annotate AnnBuilder Annotation Organism annotate AnnBuilder

updated 20.7 years ago • Francois Pepin

and flow cytometry. Who we are: Development Sciences (DevSci) is a translational science organization that plays a critical role both in Genentech Research and Early Development (gRED) and late stage development...for contributing to and helping drive data lifecycle management projects that enable the storage, organization, dissemination, and analytics of data in alignment with the scienti…

spatialtranscriptomics singlecellsequencing datamanagement FAIR computationalbiology

updated 3.8 years ago • nwalton

<div class="preformatted">This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - July 30, 2003 - Met…

Annotation Annotation

updated 22.3 years ago • madman@jimmy.harvard.edu

myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "custommice", pkgPath = myDir, organism = "Mus musculus", version = "1.1.0", author = list(authors = "Yihuan Xu", maintainer = "yihuan.xu at jefferson.edu"), fromWeb = TRUE

Organism annotate AnnBuilder Organism annotate AnnBuilder

updated 18.3 years ago • Yihuan Xu

_454\_v3.1.1.repeatmasked\_assembly\_v3.0.1.gff3", format = "gff3", dataSource = "Phytozome v12.1", organism = "Sorghum bicolor") then: promoter <- getPromoters(TxDb = Sb\_TxDb, upstream = 2000, downstream = 2000, by = "gene") When I try to

software error bioconductor

updated 7.7 years ago • sarit.weissmann5

On behalf of the [Bioconductor conference organizing committee](http://bioc2020.bioconductor.org/organizers

bioconductor conference event News

updated 5.9 years ago • shepherl

of using GO slims instead of raw (total amount of GOs available in  gene universe of the organism of interest) GOs population ?  Which pros and cons has each from the mentioned above approaches ?&nbsp

topgo

updated 10.2 years ago • s.apocarpum

I am trying to do BLAST (dna-nucleotide) for a sequence. I want to a sequence with the rhesus organism. I would like to get the following values: 1. Score (bits) 2. E-value 3. # Matches I am trying to use the 'annotate' package with

Organism Organism

updated 13.3 years ago • Tim Smith

the TSS. I use the below statement for retrieving the 1000 bp upstream region from the TSS for yeast organism. seq=getSequence(id="R0010W",type="ensembl_gene_id",seqType="coding_gen e_flank",upstream=1000,mart = mart); Now my question

Yeast Organism biomaRt Yeast Organism biomaRt

updated 15.0 years ago • Kishor Tappita

bam$") > bamfiles [1] "490224.bam" "490225.bam" > rnaSeq <- easyRNASeq(filesDirectory=getwd(), + organism="Hsapiens", + chr.sizes=chr.sizes, + readLength=58L, + annotationMethod="biomaRt", + count="exons", + filenames=bamfiles[1], + …

RNASeq Cancer Organism easyRNASeq RNASeq Cancer Organism easyRNASeq

updated 13.1 years ago • Richard Friedman

I'm trying to do pathway analysis for RNA-seq data (KEGG, GSEA, GO). My organism is Bacteroides thetaiotaomicron and I'm having trouble finding an annotation database. AnnotationHub has one...I also tried creating a library using AnnotationForge, which gave me files containing seemingly all organisms and produced an error message: > makeOrgPackageFromNCBI(version = "0.1", + …

annotation rna-seq pathway analysis

updated 5.2 years ago • microPhD

<div class="preformatted">Hi, I would appreciate help with the following. I was following the vignette "How to use AnnBuilder". I tried to adapt this to my goal of creating an annotation data package with the Unigene Identifiers. I made some very minor changes and used the file samclonegb2 which is just a small text file with the first column being a list of IMAGE cloneIDs and the second …

Annotation Organism PROcess Annotation Organism PROcess

updated 22.0 years ago • Law, Annie

Hi, I've been following the example for using __GOstats__ at its manual at __https://www.bioconductor.org/packages/release/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf.__ Unfortunately I have an error <pre> <em>Error in initialize(value, ...) : invalid names for slots of class “GOHyperGResult”: pvalues, oddsRatios, expectedCounts, catToGeneId, organism</…

GOstat GOstats

updated 9.5 years ago • ccanchaya

Dear All,      I am planning to create an annotation package for the organism Heterorhabtidis bacteriophora. I have downloaded all the necessary files of around 85 GB from NCBI using the AnnotationForge

AnnotationDbi AnnotationForge

updated 14 months ago • KABILAN

My organization's IT policies have tightened up with regard to making external connections, and I'm getting errors like localHub

celldex

updated 4.2 years ago • swbarnes2

file = "Homo_sapiens.GRCh38.105.gtf.gz", format="gtf", dataSource="Ensembl", organism="Homo sapiens") GuitarPlot(txTxdb = txdb, stBedFiles = stBedFiles, headOrtail = TRUE, enableCI = FALSE, mapFilterTranscript

Guitar

updated 3.8 years ago • 建国

selected to calculate the back ground model, also be promoter sequences of the same(and of the same organism)probes? Regards, Prashantha Hebbar Kiradi, Manipal Life Sciences Center, Manipal University, Email:prashantha.hebbar

probe cosmo probe cosmo

updated 15.8 years ago • Prashantha Hebbar

coverage and >90% identity. Is there program in R to select them? I want to detect number of organism showing uniques results for given sequences.  Thanks. Dr. Ghorpade Prabhakar B. PhD Scholar ( Veterinary Biochemistry

Coverage Coverage

updated 11.6 years ago • prabhakar ghorpade

Hi I want to use GenomicFeatures to extract upstream sequences from a genome using gene\_IDs My organism (Anopheles melas) has an assembled genome (fasta) and a gtf file. It seems like these are all the files I should need, however

genomicfeatures

updated 8.2 years ago • david.rinker

command. This is my code spia_result <- spia(de=sig_entrez, all=background_entrez, organism="hsa") head(spia_result, n=5) plotP(spia_result, threshold=0.1) whereas the two vectors are of entrez genes. It all works

SPIA functional-analysis Pathways KEGG

updated 5.7 years ago • Assa Yeroslaviz

analysis. But my project is about metatranscriptome. There are many different known and unknown organisms. Is it still possible to do GO enrichment

edger go rnaseq

updated 8.8 years ago • y.zhang36

LAEVIS. For alignment I used mRNA sequence from genebank. Is it possible to do tx2gene for this organism? it is absent here ftp://ftp.ebi.ac.uk/pub/databases/gencode/ and even here https://bioconductor.org/packages/release

deseq2

updated 6.3 years ago • Daria

package does not seem to have a method to create it from GFF. (we work with non model organisms, so no ucsc/biomart available for us). I should be able to create it with 'makeTranscriptDb(transcripts, splicings

TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures

updated 13.4 years ago • gowtham

attempting to use the GOstats package to do a differential KEGG pathway analysis in wheat (non-model organism without an organism package). I'm following the guidelines from GOstats for unsupported organisms [here][1]. The problem

AnnotationDbi GOstats

updated 13 months ago • a1869161

Hi, I am using the topGO package and this is my code: <pre> # input data head(dat) ID Entrezid Ensembl logFC AveExpr t P.Value adj.P.Val B fc ctrl 1 17500195 20845 ENSMUSG00000031574 1.350722 8.794343 35.00267 3.322001e-09 2.994419e-05 11.46955 2.550397 8.148782 2 17514553 17394 ENSMUSG00000005800 1.474257 7.718298 34.…

topgo org.mm.eg.db

updated 10.4 years ago • komalr