Bioconductor Forum

post-doctoral-research-fellow/job Fred Hutchinson Cancer Center is an independent, nonprofit organization providing adult cancer treatment and groundbreaking research focused on cancer and infectious diseases

JobPosting

updated 13 months ago • Fred Hutch (Recruiting)

fail to download KEGG data... Error in download.KEGG.Path(species) : 'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'... 此外: Warning message: In utils::download.file(url, quiet

quiet=T):InternetOpenUrl失败:’无法与服务器建立连接' 报错描述：Warningmessage:Indownload.file(xml.url xml.target

updated 4.0 years ago • LeeYusheng

genome as provided by YU (V3.3, Jan. 2011) # and will store in Biostrings objects. Version: 1.0.0 organism: clof species: insect provider: YU provider_version: Assembly V3.3 release_date: Jan, 2011 release_name: insects

BSgenome Biostrings BSgenome BSgenome Biostrings BSgenome

updated 14.9 years ago • Steve Shen

<div class="preformatted">>Dear Adi and all members, >I have been trying to analyze and identify unique genes and their association with signal pathways by using SPIA package. Here is the link of one of the pathways that I generated: >http://www.genome.jp/dbget- bin/show_pathway?hsa04530+5578+3993+4629+5590+5728 >In this table, there are several gene products …

Pathways Organism SPIA Pathways Organism SPIA

updated 14.1 years ago • Tarca, Adi

gt; testVec<-c(-0.81) > names(testVec)<-c(108101) > viewPathway(path2vis,organism="mouse",readable=T,foldChange=testVec) > sessionInfo() R version 3.5.2 (2018-12-20) Platform: x86_64-apple-darwin15.6.0

ReactomePA

updated 6.9 years ago • santos22903

baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "mu11ksuba", pkgPath = ".", organism = "Mus musculus", version = "1.0", author = list(author = "dbeyer", maintainer = "dbeyer at u.washington.edu"), fromWeb = TRUE) Error

Organism mu11ksuba annotate limma gcrma matchprobes annaffy AnnBuilder Organism mu11ksuba

updated 19.8 years ago • Dick Beyer

severe batch effects (at least during library prep and sequencing). However since it's a non-model organism study (veterinary field) I thought that SVA might maybe account for mixed breeds within the groups or other unknown

DESeq2 sva svaseq batch effect correction

updated 7.9 years ago • L_K

data). Regards- Rory From: Doron Betel <dob2014@med.cornell.edu<mailto:dob2014@med.cornell.edu>> Organization: WCMC Date: Fri, 1 Feb 2013 18:05:02 -0500 To: Rory Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk

DiffBind DiffBind

updated 12.9 years ago • Rory Stark

clusterprofiler. I used top 50 upregulated genes with ENSEMBL ID to show this preoblem.  The organism I used was non-mode animal sheep (Ovis aries). So I created the OrgDb first. And then I used this OrgDb to do GO enrichment

clusterprofiler go enrichment functional enrichment

updated 7.1 years ago • Jack

I'm using version 1.4.18 under linux) or the sources used for annotation (I used getSrcUrl("all", organism="Mus Musculus") to src the various annotation files) that would explain these results? Best, Jeff __________________________________

Annotation moe430a moe430b probe AnnBuilder Annotation moe430a moe430b probe AnnBuilder

updated 21.2 years ago • Jeffrey Rasmussen

<div class="preformatted">Hi, I've asked about this before and got hardly any response, so I'll try again. I guess this is universal but I'm using affymetrix arabidopsis ATH1 data in my examples. Most (all?) normalisations assume that the different samples are similar, with the majority of probesets not changing. So the question is what to do when lots of them are changing due to differen…

oligo oligo

updated 21.5 years ago • Matthew Hannah

c("SRR000648","SRR000657"), srcType = 'ftp' ) study sample experiment run analysis organism instrument.platform instrument.model library.name library.layout 1 SRP000098 SRS000290 SRX000122 SRR000648...downloaded 133 Kb study sample experiment run analysis organism instrument.platform instrument.model library.name library.layout 1 SRP000098 SRS000290 SRX000122 SRR0…

Genetics SRAdb Genetics SRAdb

updated 12.6 years ago • Jack Zhu

lt;- UG(srcUrl = ugUrl, parser = file.path(pkgpath, "scripts", "gbUGParser"), baseFile = "geneNMap", organism = "Homo sapiens", built = "N/A", fromWeb = TRUE) srcObjs[["eg"]] <- eg srcObjs[["ug"]] <- ug llMapping <- parseData(eg, eg at accession) -- Benjamin

AnnBuilder PROcess biomaRt AnnBuilder PROcess biomaRt

updated 19.0 years ago • Benjamin Otto

**Job Posting Description** At Boston Children's Hospital, success is measured in patients treated, parents comforted, and teams taught. It's in discoveries made, processes perfected, and technology advanced. In major medical breakthroughs and small acts of kindness and in colleagues who have your back and patients who have your heart. As a teaching hospital of Harvard Medical School, our reac…

job bioinformatics Job

updated 6.6 years ago • shira.rockowitz

know where to look for the map. I guess the way you created gss means that it doesn't know about the organism you're using, and EntrezIdentifier() also doesn't. What you want is > mapIdentifiers(gss, EntrezIdentifier("org.Mm.eg.db

Cancer affy Cancer affy

updated 17.6 years ago • Martin Morgan

logFC > names(HIF1a)=as.vector(tg1$ENTREZ) > HIF1a1=x$ENTREZ > res=spia(de=HIF1a,all=HIF1a1,organism="hsa",nB=2000,plots=F,beta=NUL L,combine="fisher",verbose=F) > res Name ID pSize NDE pNDE tA pPERT pG pGFdr pGFWER Status

Microarray SPIA Microarray SPIA

updated 14.4 years ago • Jing Huang

has length zero."   My file has 98 plates, each with 380 detectors. Here is a snippet of the organization of the tab delimited txt file _Sample Detector Cq_ _CAV\_Plate\_55 ath\_miR159a\_000338 Undetermined_ _CAV

norm.qpcr microrna troubleshooting

updated 7.9 years ago • leet

any interviews right after her initially spherical gain and was fined $15, 000 as a result of event organizers. Best individuals versus every single of the Grand Slam tournaments arrived jointly toward compose a assertion...saved towards a substantial traditional than your self and I are. The letter in opposition to event organizers seems to be toward me in direction of generate experience Though…

FlowSorted.DLPFC.450k

updated 21 months ago • Gp.dispoz

Hello everyone, I am PhD student working on performing GSEA analysis for *Candida albicans* data. I queried AnnotationHub for existing records and found none. Hence I am trying to make an Organism DB for *C. albicans*. After going through the threads of https://support.bioconductor.org/p/9148255/#9155272; https://support.bioconductor.org...data. I queried AnnotationHub for existing records and…

OrgDb AnnotationForge

updated 20 months ago • Gayatri

Version="0.0.1", PkgTemplate="NCBIORG.DB",AnnObjPrefix="org.Pseudomonas aeruginosa PAO1.eg",organism="Pseudomonas aeruginosa",species="Pseudomonas aeruginoa PAO1") # include your problematic code here with any corresponding

AnnotationHub AnnotationForge Pseudomonas_aeruginosa

updated 3.1 years ago • Manmohit

Version="0.0.1", PkgTemplate="NCBIORG.DB",AnnObjPrefix="org.Pseudomonas aeruginosa PAO1.eg",organism="Pseudomonas aeruginosa",species="Pseudomonas aeruginoa PAO1") # include your problematic code here with any corresponding

AnnotationHub AnnotationForge Pseudomonas_aeruginosa

updated 3.1 years ago • Manmohit

a new analysis, it asks me if I want to use APT for gene/exon summaries. I click "yes" and chose the organisms (in my case, Hs). Next, I select the working directory, the target file and answer "no" to the question "are you using genechips

Microarray Normalization GO probe oneChannelGUI Microarray Normalization GO probe

updated 15.4 years ago • ifig319@ifi.csic.es

<div class="preformatted">Dick Beyer <dbeyer <at=""> u.washington.edu> writes: > > Hi, > > I get the "Error in pathIDsLev1" error when using the gene2pathway retrain() function. > > > retrain(minnmap=30, level1Only="Metabolism", level2Only="Genetic Information Processing", > organism="hsa", gene2Domains=NULL, KEGG.pack…

updated 15.8 years ago • Jean-Pierre Desvignes

7) Strong communication skills and ability to collaborate with cross- functional teams across the organization 8) Strong desire to work in a high-energy, hands-on startup environment Education: MS or PhD in statistics, bioinformatics

Genetics Genetics

updated 13.4 years ago • Rong Chen

out soon. Sincerely, Dr. Kent Weigel and Dr. Guilherme Rosa Symposium co-chairs The Symposium organization acknowledges funding support from the USDA- NRI 43.0 Animal Genome Program. -- Guilherme J. M. Rosa Assistant Professor

Genetics Genetics

updated 17.1 years ago • Guilherme J. M. Rosa

for Schizosaccharomyces pombe (fission yeast) as provided by Pombase (ASM294v2)", Version = "2.0", organism = "Schizosaccharomyces pombe", common_name = "Fission yeast", provider = "Pombase", provider_version = "ASM294v2", release_date

bsgenome MutationalPatterns

updated 5.7 years ago • sibyl.bertrand

functions in the lumi package. As for the functions of modeling methylation status, I will organize and upload them to the developing version within next few weeks, hopefully by the end of this year. For the Illumina

Microarray lumi BRAIN Microarray lumi BRAIN

updated 14.8 years ago • Ina Hoeschele

HI all. I am trying to run derfinder, but am running into a problem with its calls to AnnotationDbi. I seem to have isolated the problem like so: <pre> > library ("AnnotationDbi") > load("dogTxEnsembl.Rda") > class(dogTx) [1] "GenomicFeatures" > organism(dogTx) Error in sqliteSendQuery(con, statement, bind.data) : expired SQLiteConnection</pre> I…

annotationdbi

updated 10.6 years ago • jessica.hekman

mySrcUrls, baseMapType = >myBaseType, + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, + organism = "human", version = "1.1.0", makeXML = TRUE, + author = list(author = "myname", maintainer = "myname@myemail.com"), + fromWeb = TRUE) Error

GO Organism AnnBuilder GO Organism AnnBuilder

updated 20.9 years ago • Giulio Di Giovanni

i.e. I get 2442 GO from 642 genes, I want 642 max (some won't have any MF level 2 I think)). My organism is Plasmodium. I also tried through the org.Pf.plasmo.db package too, but I don't think there is a way to select a specific

GO Organism biomaRt GOSim GO Organism biomaRt GOSim

updated 14.4 years ago • Olivier Lucas

and computational infection research.</p> <p>The lab develops software and algorithms, co-organizes the Critical Assessment of Metagenome Interpretation challenge (CAMI; <a href="https://data.cami-challenge.org

job bioinformatics computational biology post-doc postdoc Job

updated 9.2 years ago • cristina della beffa

<div class="preformatted">Hi, I am trying to make a pd.info package for the Affy Primeview array, but I get an error. Thanks for any help! Cheers, Max This is my code: library(pdInfoBuilder) cdf <- list.files( pathAnnotPr, pattern = ".cdf", full.names = TRUE ) cel <- list.files( pathC, pattern = ".CEL", full.names = TRUE )[1] # take first array tab <- list.file…

BiocViews Annotation Cancer Organism cdf probe affy biocViews BiocViews BiocViews Cancer

updated 12.5 years ago • Max Kauer

baseName = myBase, baseMapType = myBaseType, pkgName = "hs95av2Entrezg7", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "Weijun", maintainer = "Weijun <luo_weijun at="" yahoo.com="">"), fromWeb =T) Here

probe AnnBuilder probe AnnBuilder

updated 19.5 years ago • Luo Weijun

typeNormalized = "dataframe", typeSegmented = "dataframe", prior = "auto", nclass = 3, organism = "human") NULL > Result <- CGHcall(norm3, seg3, organism="human") Dividing chromosomes into arms: New chromosome: 1 Arm: 1...but: > Result <- CGHcall(norm3[norm3$Chromosome=="1",], seg3[norm3$Chromosome=="1",], organism="human") Dividin…

Cancer Organism MANOR oligo CGHcall BAC Cancer Organism MANOR oligo CGHcall BAC

updated 17.9 years ago • Daniel Rico

0.05, readable = TRUE) > ego_normal # over-representation test # #...@organism Homo sapiens #...@ontology BP #...@keytype ENTREZID #...@gene chr [1:350] "54541" "2027" "79633" "5097" "81565" "54508" "7580" "5048" "494470" "143425...0.05, readable = TRUE) > ego_tumor # # over-representation test # #...@organism Hom…

ChIPseeker

updated 20 months ago • Henry

below: The study [GSE13465][1] contains experiments of toxic effects of acetaminophen on two organisms: ?- human ?- rat I only care about data from the rat cultures. (The human data is present due to submitter error.) The rat cultures...GSM339451_Cy3_37374.txt GSM339451_Cy5_37374.txt ????????????????????????????? GEOSample????????? Organism Donor?? Medium Cy3APAP ??? Std_APAP0.vs.Std_APAP0.2?…

Microarray Organism limma oligo Microarray Organism limma oligo

updated 14.5 years ago • Chris Lasher

if I could even get some expressed regions data, I think I uncovered an issue people working with organisms not presently in the "GenomeInfoDbData" may encounter. In trying to troubleshoot I saw that [in order to deal...my chromosome names be in the same order as GenomeInfoDb needs them, if I simply insure my source organism is not in the database, I'll be able to at leat build a regi…

derfinder GenomeInfoDb GenomicRanges

updated 8.7 years ago • Wayne

Marketing, Agriculture, Aromatic Plants, Ayurveda, Bio-fuel, Environment, Herbs, Medicinal Plants, Organic Farming, Pharmaceutical, Seed-technology, Spices. We are selling the above publications not only to make money but...Essential oils obtained from aromatic plants by distillation expression or extraction with suitable organic solvents represents a complex mixture of several compounds. A vast …

updated 16.3 years ago • Sanjeev Prajapati

**PhD-position in bioinformatics / computational biology (75% E13) at Ruhr-University Bochum** The recently established [Computational Phenomics group][1] led by Prof. Dr. Arne Sahm uses bioinformatics methods to study the aging process. For example, we are assembling genomes of exceptionally long-lived species to identify evolutionary adaptations that enable these species to age slowly and heal…

Mergeomics Epigenome Evolution NGS Aging

updated 21 months ago • arne.sahm

in the analysis both bulk and single-cell massively-parallel RNA sequence data derived from model organisms (mouse, rat, and human). While RNA sequence analysis will be a main part of your mission, there will also be opportunities

RNA-seq Job Single-Cell

updated 4.6 years ago • rbrns

though not sure what we would learn from them if significant). Thanks for your help! ```r ## Organize data and design cnt <- DGEList(data) cnt$samples$group <- group <- sample.info$Group design <- model.matrix(~0+group

Lipidomics Metabolomics limma Normalization

updated 4.5 years ago • pgugger

KO numbers and the only column is the log2-fold change (previous analysis). I don't have a specific organism I am working with as these are results from environmental samples (shotgun metagenomic, Illumina sequencing) and

pathview KEGG parsing

updated 8.1 years ago • ladypurrsia

NIH: The NIH, comprised of 27 separate research institutes, is one of the world’s premier research organizations located in Bethesda, Maryland, just outside Washington, D.C. To find out more about the NIH, its mission, history

job Job

updated 9.8 years ago • Sean Davis

object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: UCSC # Genome: hg19 # Organism: Homo sapiens # Taxonomy ID: 9606 # UCSC Table: knownGene # Resource URL: http://genome.ucsc.edu/ # Type of Gene ID: Entrez Gene

TxDb.Hsapiens.UCSC.hg19.knownGene

updated 8.3 years ago • l.selfors

I am looking for **Data Engineer** who would like to join our NaturalAntibody team to work on its computational antibody drug discovery product portfolio. ****About the role**** As a **Senior Data Engineer** you will design and work on our data and analytics stacks. You will contribute to our data stack by analysing our existing databases and creating novel datasets. You will employ this …

AWS BigData Engineer python

updated 4.7 years ago • Ewa

about this package:" [36] "" [37] "DB schema: HUMANCHIP_DB" [38] "DB schema version: 2.0" [39] "Organism: Homo sapiens" [40] "Date for NCBI data: 2009-Sep1" [41] "Date for GO data: 20090830" [42] "Date for KEGG data: 2009-Sep16" [43] "Date for

GO GO

updated 15.6 years ago • David Lyon

<div class="preformatted"> Dear Maintainer, I downloaded available NimbleGen 'single channel' 532.PAIR files for a custom built expression microarray from NCBI/GEO (GPL11164). However, I get an error message when I try to make the annotation for this platform using pdInfoBuild. In pdInfoBuilder Reference Manual (June 5, 2013), under the NgsExpressionPDInfoPkgSeed method, there is a slot f…

Microarray Annotation Organism annotate pdInfoBuilder Microarray Annotation Organism

updated 12.6 years ago • Guest User

Hi, I have troubles with using tximeta from the sample table (`Cov` below). I loaded the sample table (3 columns, names (all unique), files (absolute paths to `quant.sf`) & condition (all "A")). I have created a linked transcriptome from downloaded files using: ``` makeLinkedTxome( indexDir= <abs directory="" indices="" path="" salmon="" to="">, source="Gencode…

deseq2

updated 6.2 years ago • eric.blanc

<div class="preformatted">I thought this might be of interest. Here's a forwarded message and attachment from Ola Spjuth allowing LIMMA and SMA to work as a BASE (http://base.thep.lu.se) plug-in. Please direct questions to Ola or the BASE mailing list. Lao Lao H. Saal Institute for Cancer Genetics / Herbert Irving Cancer Center College of Physicians & Surgeons, Columbia Universi…

Genetics Cancer limma Genetics Cancer limma

updated 22.3 years ago • Lao Saal

the conjoined information from miRecords and miRDB ... but it must be harder because the miRecords organization does not provide any interface library. I have attached the pruned version of miRecords xls file and my crude

GO Homo sapiens biomaRt GO Homo sapiens biomaRt

updated 16.5 years ago • mauede@alice.it

I have an output file containing upregulated genes from a non model organism ordered by adjusted p-value. ```r geneID Rp.chr4.1864 Rp.chr1.1957 Rp.chr4.2000 Rp.chrX.1597 Rp.chr4.1782 Rp.chr4.1865...IPR000618: Insect cuticle protein GO:0005576: extracellular region; GO:0007275: multicellular organism development; GO:0008010: structural constituent of chitin-based larval cuticle; GO:003…

annotation RNASeqData

updated 9 months ago • AL

nbsp;                 organism="Arabidopsis lyrata") `` Above command creates the txdb as below: <code>Import genomic features from the file as a GRanges...br/> # Supporting package: GenomicFeatures<br/> # Data source: gtf file for Arab…

bioconductor txdb maketxdbfromgff

updated 8.1 years ago • Nader.Aryamanesh

ortho_alltime_merged_temp.gtf', dataSource="orthoalltime", organism="Homo sapiens", format='gtf') I get all transcripts and exons in my annotation file: tx_by_gene <- transcriptsBy(txdb

GenomicFeatures

updated 3.2 years ago • nattzy94

multidisciplinary collaborations addressing fundamental biological questions in model and non-model organisms. The research emphasis should be on integrative approaches, such as systems biology, networks analysis, comparative

updated 19.3 years ago • Thomas Girke

A,A,B,B,B) CountsGenes_biomart<- easyRNASeq(filesDirectory=BamPath, + filenames=fls, nbCore=5, + organism='Mmusculus', + chr.sizes=as.list(seqlengths(Mmusculus)), + readLength=50L, + annotationMethod="biomaRt", + format="bam", + count

RNASeq BSgenome BSgenome easyRNASeq RNASeq BSgenome BSgenome easyRNASeq

updated 13.2 years ago • Mayte Suarez-Farinas

nchar(cleancdfname("RaGene-1_0-st-v1")) - 3)), + pkgPath = '~/R_HOME/site-library-2.8.0', organism = "Rattus norvegicus", version = "1.0", + author = list(authors = "Mark W Kimpel", maintainer = + "mkimpel@iupui.edu"), fromWeb = TRUE) Read

Annotation Organism cdf probe affy AnnBuilder Annotation Organism cdf probe affy

updated 17.2 years ago • Mark W Kimpel

com", +          genomebuild="rn6", +          organism="Rattus norvegicus", +          species="Rattus norvegicus", +          version = "0.0.1") &gt

annotation microarray pdinfobuilder oligo

updated 9.3 years ago • Ed D

data1) for (i in 1:(n-1)){ g1=data1[i] for (j in i:n){ g2=data1[j] zz=geneSim(g1, g2, ont="MF", organism="human", measure="Wang", combine="avg") similarity= paste(data1[i], data1[j], zz[[1]], sep="\t") write.table(similarity, "/pub2/nsw/zjz/genesim

R package problem

updated 10.1 years ago • zjzace

pkg), inherits = FALSE) 5: GenomeInfoDb:::.taxonomyId 4: .prepareGFFMetadata(file, dataSource, organism, taxonomyId, miRBaseBuild, metadata) 3: makeTxDbFromGFF(PARAMETERS$GENE_ANNO_GTF, format = "gtf") 2: .read.gtf(PARAMETERS

exomepeak

updated 7.3 years ago • 939930094

producing wrappers. However, I am struggling as there is no AnnotationDbi package available for this organism. I decided to finally take the plunge and try to see if I could be one myself using AnnotationForge and was quite exciting

Alignment Annotation Organism Schizosaccharomyces pombe biomaRt AnnotationForge Alignment

updated 12.4 years ago • Marco Blanchette