Bioconductor Forum

prob, author = "Javier",email = "email",biocViews = "AnnotationData",genomebuild = "NCBI Build 36",organism = "Human", species = "Homo Sapiens",url = "") makePdInfoPackage(seed, destDir = ".") And I installed the package: R CMD INSTALL pd.hugene.1.0.st.v1

Preprocessing cdf oligo oneChannelGUI Preprocessing cdf oligo oneChannelGUI

updated 16.2 years ago • Javier Pérez Florido

308", "317", "321", "506", "540", "378", "388", "396") > clusterSim(cluster1, cluster2, ont="MF", organism="human", measure="Wang") Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (expired SQLiteConnection

GO GOSemSim GO GOSemSim

updated 12.1 years ago • Guest User

Hi, I was using BSseq package to detect DMRs in non-human organism (chicken), I have a few questions that have confused me for some time: 1. The BSseq package reference manual states that

bsseq

updated 9.1 years ago • Stephen

latest) I've been working with the `biomaRt` package to get mappings between different organizations and I noticed something that, to me, seems like a bug, but I'm not sure. I'm trying to get mappings between `ensembl_gene_id

BiomaRt biomart

updated 6.4 years ago • matrs

<div class="preformatted">Dear list, I'm trying to retrieve protein orthologs for human proteins for the most common model organism (mouse,C.elegans,Drosophila,S.cerevisae,etc) such that for my work in human I can point other researchers to the appropriate...Dear list, I'm trying to retrieve protein orthologs for human proteins for the most common model organism (mouse,C.elegans,Drosophila,…

biomaRt biomaRt

updated 14.8 years ago • Stefanie Carola Gerstberger

gt; library(SPIA) > data(colorectalcancer) > res<-spia(de=DE_Colorectal, all=ALL_Colorectal, organism="hsa",pathids=c("05210","04010"),nB=2000) > res It will take a day or two before the change in the SPIA package will be reflected

SystemsBiology Pathways Cancer SPIA SystemsBiology Pathways Cancer SPIA

updated 16.1 years ago • Tarca, Adi

<div class="preformatted"> BioConductor Developer Workshop 24 - 25 April 2008 Lausanne, Switzerland This meeting is aimed at active developers as well as prospective developers interested in improving package writing skills and contributing to the BioConductor project. The workshop will be held at the University of Lausanne, Switzerland, with English as the working language. Registration…

updated 18.0 years ago • Darlene Goldstein

GeneGA(sequence=seq,popSize=40,iters=150,crossoverRate=0.3,mutationChance=0.05,region=c(1,60),organism="ec",showGeneration=FALSE)</p> <p abp="297">The error message, produced by the last line of code, is:</p> <pre abp="298"> Error in system

software error

updated 6.5 years ago • chulmelowe

Hi guys,  I've been back and forth on this with all sorts of variations, but error keeps coming up. Basically trying to create a geneLists for analysis for clusterprofiler. My numeric are Fisher's P.values from a meta analysis and the names are Gene Symbols though I did also try ProbeIDs.  Any chance you know why I'm getting the data.frame error. Oh I check manually if there w…

genelist clusterprofiler

updated 8.6 years ago • bhgyu

div class="preformatted"> ------ Forwarded Message From: Tabare Mourot <tabare.mourot@igf.cnrs.fr> Organization: IGF Date: Wed, 05 Apr 2006 09:43:22 +0200 To: Sean Davis <sdavis2 at="" mail.nih.gov=""> Subject: Re: [BioC] AnnBuilder package

AnnBuilder AnnBuilder

updated 19.8 years ago • Sean Davis

<div class="preformatted">Hello Bioc users, While our package idiogram is has been created to primarily display gene expression data (with an associated chromLocation object) you can alternatively create one on the fly. In the code below I create a mock data frame similar to Camper's and from that I generate a bare bones chromLocation object. From there you can plot the data a coup…

Organism idiogram Organism idiogram

updated 17.2 years ago • Dykema, Karl

Hello I'm using SPIA on my toptable generated by limma. I have R version 3.3.1, and updated biocLite to the latest version. It makes the results file using  res=spia(de=DE,all=ALL,organism="hsa",nB=2000,plots=FALSE,beta=NULL,combine="fisher") However, when I use plotP(res,threshold=0.05) I get the following error...biocLite to the latest version. It makes the results file u…

SPIA plotP threshold

updated 9.1 years ago • docpriya21

a single column of transcript names for Arabidopsis thaliana using our internal "orgid" filter for organism ID 167: > library('biomaRt') > phyto=useMart('phytozome_mart', dataset='phytozome') > transcripts = getBM(attributes

Arabidopsis thaliana biomaRt Arabidopsis thaliana biomaRt

updated 14.3 years ago • Richard Hayes

paper submission For more information, please visit http://www.camda2009.org Sincerely, CAMDA2009 organizers [[alternative HTML version deleted]] </div

Sequencing Sequencing

updated 16.4 years ago • Pan Du

a 2 x 2 x 2 factorial arrangement. Objective: Compare the differences in gene expression in each organ (HG or TC) within each timepoint (24 or 48). For that, analyze main factors interactions or if they act together on each gene...in each organ/timepoint. edgeR approach used: Experiments with all combinations of multiple factors The groups: ``` [1] CM.14.NO CM.14.NO

edgeR

updated 22 months ago • tsl0026

TRUE/FALSE needed In addition: There were 11 warnings (use warnings() to see them) > gpQuality(organism = "Hs") [1] "Starting gpQuality..." Error in if (abs(MMR[i]) > 0.5) numSpotOverMmrLim <- numSpotOverMmrLim + : missing value where...gt; traceback() 2: slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG) 1: gpQuality(organism = "Hs") > warnings() Warnin…

Microarray Microarray

updated 11.4 years ago • Guest User

hub <- AnnotationHub:::AnnotationHub() ## Query for the specific database (organism & sqlite) query_result <- AnnotationHub:::query(hub, c("Heterorhabditis", "bacteriophora", "sqlite")) ## Assuming the SQLite

AnnotationDbi AnnotationHub Annotation AnnotationForge

updated 14 months ago • KABILAN

and GFF files). So, I'm doing this: ``` txdb <- makeTxDbFromGFF (file = GFF_FN, dataSource="...", organism="Saccharomyces cerevisiae") seqinfo <- Seqinfo (seqnames = c(...), seqlengths=c(...), isCircular=c(...), genome="..") vcf <- readVcf (VCF_FN

R VariantAnnotation

updated 3.3 years ago • rwan.work

ALL",pvalueCutoff = 0.05,qvalueCutoff = 0.05, readable = T) KEGG<-enrichKEGG(gene$ENTREZID,organism = KEGG_database,pvalueCutoff = 0.05,qvalueCutoff =0.05) barplot(KEGG,showCategory = 30,title = 'KEGG Pathway') barplot

RNASeq

updated 4.0 years ago • waltsonwang88

Program Committee: Robert Gentleman, Darlene Goldstein, Wolfgang Huber, Victor Jongeneel Local Organizer: Darlene Goldstein Sponsors: Hewlett-Packard and Intel -- Darlene Goldstein ?cole Polytechnique F?d?rale de Lausanne

Annotation Biobase Annotation Biobase

updated 18.9 years ago • Darlene Goldstein

be very useful to be able to be able to deal with values that are greater than 2^32 (≈ 10^9) as many organisms have genome size longer than that. __Question__ - Am I right to think that this is an integer overflow issue? - Do you

iranges r

updated 9.8 years ago • remi.b.md

<div class="preformatted">Dear all,* * enrollment is open for 4 PhD positions in cancer computational biology at the IFOM-IEO campus in Milan, see the ad below. Best, mattia ** *############################# * * * *Cancer computational biology* Four PhD positions in Computational Biology are available at the IFOM- IEO Campus in Milan. The candidates will have the opportunity to wor…

Sequencing Epigenetics Cancer Sequencing Epigenetics Cancer

updated 14.3 years ago • mattia pelizzola

nbsp;  0.000    7.597    5    30    789    organ morphogenesis Which test genes (entrez ids) were present in 'tissue developemnt'? Is is possible? Thanks in Advance

GO

updated 11.0 years ago • Bade

<div class="preformatted">Hi, Aric, I moved the conversation here because other people might be benefit from it. Similar to rangeGate() and quandrantGate(), an extra argument 'plot' is added to lymphGate() to produce plots of filter results. This update is included in flowStats V 1.7.4 in the Bioc-devel branch. -------- Original Message -------- Subject: Re: flowStats update ?ly…

Cancer flowStats Cancer flowStats

updated 15.5 years ago • Chao-Jen Wong

1235745522981523457?s=20 ## English version (en inglés) ``` Do you want to learn how to organize your R code 👨🏽‍💻 and analyze 👩🏽‍💻single cell RNA sequencing data with @Bioconductor? Save the date! See you August 3-7 🗓 Instructors

CDSB Mexico Workshop News

updated 5.8 years ago • Leonardo Collado Torres

Please circulate widely. UC Irvine's newly created Research CyberInfrastructure Center (RCIC) is seeking a Director to oversee it's growth and increasing influence in supporting research via digital services. The RCIC will serve as the central resource for accessing, providing, coordinating and enhancing research Information Technology facilities and services for the University of California, I…

director research computing UC Irvine Job

updated 8.5 years ago • hjmangalam

factor activity nucleus Probe Set ID 220184_at GeneChip Array Human Genome U133 Plus 2.0 Array Organism Common Name Human Probe Design Information Transcript ID g13376297 Sequence Type Exemplar sequence Representative

Transcription Annotation GO hgu133a probe Transcription Annotation GO hgu133a probe

updated 21.4 years ago • Mayte Suarez-Farinas

<div class="preformatted">I am trying to make annotation package for my array platform using AnnotationDbi package. I prepared txt file that links customID and unigene. The table I am trying to import here has only 2 columns; one is gene id (CLIGG_00001) and the other is unigene id (Gga.1). I tried all I could google out and many as.character or bimap options...Here is the R output: &…

Annotation affy Annotation affy

updated 14.8 years ago • Dana.Stanley@csiro.au

booklet\_advance\_RNAseq\_2015.pdf Registration deadline April the 1st 2015 The Organizer Raffaele A Calogero   ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie

rnaseq mirna onechannelgui chimera News

updated 11.0 years ago • raffaele calogero

<div class="preformatted">Hi All I am trying to build an annotation library for some in-house plant microarrays using AnnBuilder. I have a base file that consists of a column of probe names, and nearest matches to NCBI genes. I have installed entrex files, unigene files and go files locally to speed the process. I am trying to map the plant probes on the microarray to rice genes in UniG…

Microarray Genetics Annotation GO probe AnnBuilder PROcess Microarray Genetics Annotation

updated 19.8 years ago • ross.chapman@dpi.vic.gov.au

use GSEABase to accomplish this. Oh, one last thing to add, all of our work is with non-model organisms with limited/non-existent genomic resources. So, I do have UniProt IDs associated with these gene/transcript IDs

gseabase go gene ontology goslim

updated 5.9 years ago • samwhite

mySrcUrls, baseMapType = myBaseType, otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "myname", maintainer = "myname at myemail.com"), fromWeb = TRUE) I result

GO Organism AnnBuilder GO Organism AnnBuilder

updated 19.0 years ago • Martin Kircher

of googling around. That's what I've done so far: countTable <- easyRNASeq(filesDirectory=getwd(), organism="Hsapiens", annotationMethod="rda", annotationFile="gAnnot.rda", gapped=TRUE, count="genes", summarization="geneModels...of 51 bp. [...] Preparing output Wa…

Annotation Organism edgeR DESeq easyRNASeq Annotation Organism edgeR DESeq easyRNASeq

updated 12.6 years ago • Gabriele Zoppoli

<div class="preformatted">hi all, I'm building a custom annotation service, and have encountered the following problems. Upon Reading the SQLForge.pdf vignette, i decided that i would not choose to use these functions popHUMANCHIPDB populateDB but instead build my own SQLite Database following the Database Schema Version 1.0 described in AnnotationDbi/inst/DBschemas/schemas_1.0/HUMANCH…

BiocViews Genetics Annotation GO Organism biocViews AnnotationDbi BiocViews BiocViews GO

updated 15.6 years ago • Julian Lee

AnnotationHub

updated 9.3 years ago • Jenny Drnevich

actually all the genes in my transcriptome since I used the same data to assemble it) - since my organism is not supported by GOseq, I created a vector with gene lengths from tximport count matrix with ```lengthData <- rowMeans

goseq

updated 3 months ago • f

design and interpretation of disease transcriptomics and genome sequences in humans and model organisms. Building your career together with a cohesive, interactive team of highly experienced bioinformaticians, you

job bioinformatician job bioinformatics core Job

updated 8.1 years ago • Mark Dunning

vary across clinical categories. 4. Are there recurrent sequences that do not align to known organisms for a particular cancer type. This will give the intriguing possibility of discovering brand new bacteria that

PhD cancer genomics bacteria pathogens Job

updated 8.8 years ago • Daniel Brewer

Description.Full.genome.sequences.for.Rhinella.marina..cane.toad..as.provided.by.UNSW..RM170330.. 1 organism:Rhinella marina 2 Description.Full.genome.sequences.for.Rhinella.marina..cane.toad..as.provided.by.UNSW

software error

updated 5.3 years ago • jiazhou0116

K_geneID)) %>% pull(K_geneID) %>% as.character() %>% enrichKEGG(gene=., organism="ko", universe=koalaList$K_geneID) enriched@result %>% as.tibble() %>% dplyr::select(-geneID) %>% arrange(desc(Count)) ID Description

clusterProfiler

updated 6.2 years ago • lindseypieper

annotation gff file (or similar), for a genome that is not included in the UCSC catalog of reference organisms (as is the case of this bacteria I have to analyze)? Thanks in advance JL PD. I came across "Rsubread" package, but... package

Alignment Annotation ASSIGN Alignment Annotation ASSIGN

updated 11.5 years ago • José Luis Lavín

1: multiple methods tables found for ‘fileName’  2: multiple methods tables found for ‘organism’" and when I use " __DESeqDataSetFromMatrix__" function, I get this error message: "__Error in slot(value, what) :&nbsp

deseq2 DESeqDataSetFromMatrix software error

updated 7.6 years ago • nazaninhoseinkhan

diet), I need to adjust for age, sex and possibly body mass index. That is an example of my data organization ``` Sample ID Timepoint Metabolite change_metabolite Sex Age BMI 1a 1 1 10,3000 0,0000 1 56,5 38,1 1b 1 2 20,1000 9,8000

edger

updated 5.3 years ago • anna.cot.anna.cot

makeTxDbFromGFF("/home/inah/MESA\_mRNAseq\_New/gencode.v28.long\_noncoding\_RNAs.gtf", format="gtf",organism="Homo sapiens") exons.list.per.gene <- exonsBy(txdb,by="gene") exonic.gene.sizes <- lapply(exons.list.per.gene

GenomicFeatures TPM FPKM lncRNA

updated 7.6 years ago • Ina Hoeschele

to add "ORF IDs to Chromosomal Location" to my data frame named genes in the DGEList-object. The organism is yeast, and I downloaded org.Sc.sgd.db.. ``` > columns(org.Sc.sgd.db) [1] "ALIAS" "COMMON" "DESCRIPTION" "ENSEMBL" "ENSEMBLPROT...Number of mapped keys for the maps in package org.Sc.sgd.db org.Sc.sgdORGANISM The Organism for org.Sc.sgd org.Sc.sgdPATH …

org.Sc.sgd.db

updated 2.1 years ago • Chih

combinations. While the four types of controls are basically the same strain/species of untreated organisms, they came however from different batch of lab organisms in different season/year so are likely different to some

limma limma

updated 12.9 years ago • RLW

combinations. While the four types of controls are basically the same strain/species of untreated organisms, they came however from different batch of lab organisms in different season/year so are likely different to some

limma limma

updated 12.9 years ago • RLW

is going to be difficult, because there are many different annotation formats and many different organisms specificity. It is very frequently necessary to make custom annotations because users have different questions...you are seeing above is telling you. To decide whether this is critical or not depends on your organisms and on the cases where these occur; e.g. in drosophila, poplar, these are …

Coverage Annotation GO Cancer Organism edgeR DESeq GenomicRanges Rsubread easyRNASeq GO

updated 12.1 years ago • Gordon Smyth

Thanks! ```r > forgeBSgenomeDataPkgFromNCBI(assembly_accession="GCA_002863925.1", + organism="Equus caballus") Error in find_NCBI_assembly_ftp_dir(assembly_accession, assembly_name = assembly_name) : unable

BSgenomeForge non-modelorganism unabletofindFTPdir

updated 13 months ago • Geetha

Hello, Can someone help me to subset each first intron (only) from a GRangesList representing intronsByTranscript? I've been somewhat out of practice for a period of time, and I'm stuck. Thanks, ``` 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: ASM773564v1 #…

GenomicRange GenomicRanges

updated 23 months ago • mat149

lt;- df2$log2FoldChange kegg_organism = "ath" kk2 <- gseKEGG(geneList = kegg_gene_list, organism = kegg_organism, nPerm = 10000, minGSSize = 3, maxGSSize = 800, pvalueCutoff = 0.05, pAdjustMethod = "none", keyType = "ncbi-geneid

clusterProfiler KEGGgraph clusterpr KEGG pathview

updated 3.5 years ago • rama

reconstructed metabolic networks will improve insight in the molecular functioning of a cell or an organism. Moreover, such networks might reveal disease progression, efficacy of treatments, effects of interventions and

Metabolomics Network Organism Metabolomics Network Organism

updated 16.8 years ago • Hendriks, M.

mailing list. I'm trying to use ChIPpeakAnno to identify the annotation of ChIP-Seq peaks for an organism that does not have an annotation package. I have used makeTranscriptDbFromGFF to create a transcriptDb object

Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno

updated 12.5 years ago • Alan Smith

Andrew Beggs", email = "a.beggs at bham.ac.uk", biocViews = "AnnotationData",genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens", url = "http://www.biostat.jhsph.edu/~bcarvalh") makePdInfoPackage(seed, destDir = ".") -- output

BiocViews biocViews pdInfoBuilder BiocViews BiocViews biocViews pdInfoBuilder

updated 13.2 years ago • Guest User

I am working with __MEDIPS__ bioconductor. I was able to successfully create a custom BEE genome (I know its already there in MEDIPS, but for some reason I wanted to make a different one myself). The genome folder consists of 16 separate fasta files for each chromosomes named like chr1, chr2 and so on. The seed file is given below: <pre> Package: BSgenome.Amellifera.UCSC.apiMe1 Title: …

MEDIPS

updated 9.1 years ago • Vijay Lakhujani

myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "custommice", pkgPath = myDir, organism = "Mus musculus", version = "1.2.0", author = list(authors = "Yihuan Xu", maintainer = "Yihuan XU <yihuan.xu at="" jefferson.edu="">"), fromWeb

Organism annotate AnnBuilder Organism annotate AnnBuilder

updated 18.2 years ago • Yihuan Xu

Author = author, Maintainer = maintainer, PkgTemplate = "ORGANISM.DB", AnnObjPrefix = dbName, organism = paste(genus, species), species = paste(genus, species), biocViews = "annotation", manufacturerUrl = "no manufacturer", manufacturer

BiocViews GO Organism ChipName biocViews BiocViews BiocViews GO Organism ChipName

updated 13.8 years ago • Guest User

are no mismatch probes. We estimate background with a subset of probes that target a very different organism and are essentially negative controls. These 'background' probes are randomly distributed so they broadly sample

Organism vsn limma Organism vsn limma

updated 19.1 years ago • Wolfgang Huber

pre> # Db type: TxDb # Supporting package: GenomicFeatures # Data source: test.gff3 # Organism: NA # Taxonomy ID: NA # miRBase build ID: NA # Genome: NA # transcript_nrow: 17660 # exon_nrow: 66022 # cds_nrow: 62514 # Db created

genomicranges txdb genomicfeatures featureextraction

updated 9.7 years ago • wd

http://www.bioinformatica.unito.it/RNAseq.course.html or contact : raffaele.calogero@unito.it The Organizer Raffaele Calogero -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit MBC Centro di Biotecnologie Molecolari

RNASeq RNASeq

updated 12.0 years ago • raffaele calogero