Bioconductor Forum

gene <- names(geneList)[abs(geneList) > 2] kk <- enrichKEGG(gene = gene, organism = 'hsa', pvalueCutoff = 0.05) colnames(kk@result) > colnames(kk@result) [1] "category" "subcategory" "ID" "Description" "GeneRatio

DOSE ReactomePA

updated 14 months ago • Yifeii.Ge

Hello, I have 9 samples of RNAseq data from a non-model organism (a type of fish, not zebrafish or medaka). Of these 9 samples, 4 are control and 5 are treated, all male. I have gone through

edgeR RNASeq RNASeqData Bioconductor

updated 2.8 years ago • Rebekah

Dears, I have trouble to read gtf files with branchpointer::gtfToExons While the supplied example file (gencode.v26.annotation.small.gtf) can be read, my own gtf files or any change in the example file lead to "Error: subscript contains invalid names". E.g. keeping only the gene_id and transcript_id from the example file renders it unreadable. I suspect that gtfToExons relies on specific at…

gtfToExons "Error:subscriptcontainsinvalidnames" gtf branchpointer

updated 4.3 years ago • frank.maiwald

efoss@fredhutch.org", biocViews = "AnnotationData", genomebuild = "sacCer1", organism = "Yeast", species = "Saccharomyces cerevisiae") makePdInfoPackage(seed, destDir = ".") install.packages('pd.sc03b.mr.v03

oligoClasses oligo pdInfoBuilder

updated 4.5 years ago • efoss

to found then in rows next to the fold change, Am I wrong? and of course, if I try to run to organize in decreasing order ( "feature 3") I got this error because I have basically a list of number included in the " " not associated

r reactomePA enrichment

updated 5.6 years ago • camillab.

The molecules are organized so that isopropylamine ligands project from the layers, forming organic interlayers. This crystal structure has an infinite three-dimensional framework. The two Cl- anions bridge two CuII

bridge inveRsion bridge inveRsion

updated 18.5 years ago • Bean Y. Nat

gt; object_RNASeq <- easyRNASeq(getwd(), filename = c("sample1.sorted.bam"), + readLength = 51L, + organism = "Hsapiens", + chr.sizes = chr.sizes, + format = "bam", + annotationMethod = "env", + annotationObject = exon_range, + count = "genes", + outputFormat

RNASeq Annotation Organism BSgenome BSgenome RNASeq Annotation Organism BSgenome BSgenome

updated 13.1 years ago • Guest User

about this package:" [27] "" [28] "DB schema: ARABIDOPSISCHIP_DB" [29] "DB schema version: 2.1" [30] "Organism: Arabidopsis thaliana" [31] "Date for NCBI data: 2010-Mar1" [32] "Date for GO data: 20100320" [33] "Date for KEGG data: 2010-Feb28

Annotation GO Annotation GO

updated 15.0 years ago • Asta Laiho

Hello, I am trying to create TxDb object from gtf file but end up with the following error. I have loaded required libraries abd gtf file. > gtf <-system.file("annotation_merged.gtf.gz", package = "jcc") > bam <- system.file("../sad_merged/salmon_output/mapping.bam", package = "jcc") …

genomicfeatures

updated 6.3 years ago • bioinagesh

for clinical samples, and provide early clinical phase engagement. The translational sciences organization will be the single point of accountability for delivery of robust, scientifically-driven biomarkers in all

cancer translation ngs genomics Job

updated 10.8 years ago • jhjohnsn

BWH Longwood Medical Area 75 Francis Street Boston 02115 Job: IT/Health IT/Informatics - Management Organization: Brigham & Women's Hospital(BWH) Schedule: Full-time Standard Hours: 40 Shift: Day Job Employee Status: Regular

softwaredevelopment Job job cloudcomputing genetics

updated 4.9 years ago • Vincent J. Carey, Jr.

to deal with it? To test for under and over representation i followed the guideline for unsupported organisms (https://bioconductor.statistik.tu-dortmund.de/packages/3.4/bioc/vignettes/GOstats/inst/doc/GOstatsForUnsupportedOrganisms.pdf

gostats

updated 7.6 years ago • sven.schenk

Hi, I am using the package `GSEAbase` to import a GMT file (file with gene sets). This is working fine, but I don't understand how I can extract the 'shortDescription' of the gene sets from the `GeneSetCollection`-object. I assumed this could be done using the function `shortDescription`, but apparently this is not the case. Extracting the [ugly] `setName`, `geneIds`, or `setIdentifier` go fine.…

GSEABase

updated 6.7 years ago • Guido Hooiveld

filesDirectory=getwd(),     filenames="accepted_hits.bam.bai",     organism="Dmelanogaster",     chr.sizes=as.list(seqlengths(Dmelanogaster)),     readLength=36L, &nbsp

updated 13.1 years ago • Silav Bremos

<div class="preformatted"> Hi all and M. Carlson I am now working on an archaea, which is not a common organism. I want to use goseq to do the GO analysis of my RNAseq data.In order to creat the category mappings(relationship between...class="preformatted"> Hi all and M. Carlson I am now working on an archaea, which is not a common organism. I want to use goseq to do the GO analysis of…

RNASeq GO Organism AnnotationDbi goseq RNASeq GO Organism AnnotationDbi goseq

updated 12.2 years ago • 刘鹏飞

scratch/pmaj_index_cache") > txdb <- makeTxDbFromGFF(file=gtfPath, dataSource="EnsemblDbv97", organism="Parus major", chrominfo=chromInd) Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata...TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: EnsemblDbv97 # Organism: Parus major # Taxonomy ID: 9157 # miRBase …

tximeta BiocFileCache

updated 4.7 years ago • judith.risse

produce blank plots with no error message. The only difference in the code was it was a non-model organism so I pulled annotation information from NCBI's gtf file, which has the symbols in a column named "gene". This turns out

Glimma

updated 4.6 years ago • Jenny Drnevich

Biomathematics concerning emergent problems in Statistics/Signal Processing; - participate in the organization of national/international workshops and conferences; - supervise PhD and Master thesis students, as well as

updated 18.3 years ago • jpcosta@fc.up.pt

Momo Allo", + email = "mozemaster@gmail.com", + biocViews = "AnnotationData", + genomebuild = "LGDP", + organism = "Rice", species = "Oryza Sativa", + url = "http://www.biostat.jhsph.edu/~bcarvalh") > makePdInfoPackage(seed, destDir = ".") ====================================================================== ========== Building

BiocViews Microarray Annotation Organism biocViews BiocViews BiocViews Microarray Organism

updated 15.2 years ago • Michael MOZAR

not-for-profit Centers funded by various countries, private foundations, international and regional organizations that make up the Consultative Group on International Agricultural Research (CGIAR). We are seeking applications

Sequencing Annotation Sequencing Annotation

updated 14.4 years ago • Sarah Ayling

so="" that="" twice="" well="" without="" work=""> BTW, how about KEGG enrichment for unsupported organisms using your packages? 2013-03-19 Room 8612, The Centre for Structural and Molecular Biology, Institute of Biophysics

Biophysics Biophysics

updated 12.8 years ago • Wang Ming

I generate my own TxDb from GFF: <pre> txdb <- makeTxDbFromGFF('ref_GRCh37.p13_top_level.gff3', organism='Homo sapiens')</pre> But in this case transcripts have NC\_ id instead of chromosome names: <table cellpadding="0" cellspacing

ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 10.0 years ago • gokcen.eraslan

Biomathematics concerning emergent problems in Statistics/Signal Processing; - participate in the organization of national/international workshops and conferences; - supervise PhD and Master thesis students, as well as

updated 18.5 years ago • jpcosta@fc.up.pt

gt; > rnaSeq1 <- easyRNASeq(system.file( > "extdata", > package="RnaSeqTutorial"), > organism="Dmelanogaster", > readLength=30L, > annotationMethod="rda", > annotationFile=system.file( > "data", > "gAnnot.rda

Normalization Visualization easyRNASeq Normalization Visualization easyRNASeq

updated 12.8 years ago • delhomme@embl.de

library(BSgenome.Hsapiens.UCSC.hg19) cpgd<-Repitools::cpgDensityCalc(granges(bs),organism=Hsapiens,window = 1000) and when I look at `` min(cpgd) `` it is giving me 0 and there are several cpgd equal to zero. Does that

repitools bioconductor cpgDensityCalc

updated 8.7 years ago • divyswar01

and "diseased". For each person in each group, we collected tissues from two zones of the same organ. So my data looks like this: - normal tissue1 tissue2 - diseased tissue1 tissue2 So these are paired samples. Our questions

limma limma

updated 13.5 years ago • zeynep özkeserli

details: > count.table <- easyRNASeq(system.file( + "extdata", + package="RnaSeqTutorial"), + organism="Dmelanogaster", + readLength=30L, + annotationMethod="rda", + annotationFile=system.file( + "data", + "gAnnot.rda", + package="RnaSeqTutorial

Annotation BSgenome BSgenome easyRNASeq Annotation BSgenome BSgenome easyRNASeq

updated 12.7 years ago • Guest User

amp;newlang=1&loc - https://bio-it.embl.de/centres/csda/ EMBL is an international research organization covering many fields of modern biology. Five Computational Centres provide expertise, advice, and training

EMBL Job

updated 7.0 years ago • Wolfgang Huber

names(5): ensembl_id gene_symbol n_cells is_mito is_ribo colnames: NULL colData names(88): sample organism ... label celltype reducedDimNames(2): PCA UMAP altExpNames(0): # this crashes pb <- aggregateAcrossCells(sce, ids = colData

scran SingleCellExperiment scuttle scater

updated 5.0 years ago • enricoferrero

map, model and understand genetic networks at single cell resolution in complex tissues of organisms in vivo. The project combines high-throughput reverse genetics by inducible CRISPR-Cas9 gene knockout, single

job huber embl Job

updated 6.8 years ago • Wolfgang Huber

Hi Everyone!! I am in a pursuit to retrieve some random regions (nullset) from the hg38 genome with reserved nucleotide composition like I have in the input BED file (positiveset). I know this shouldn't be theoretically difficult, but it turns out to be otherwise. I wish to obtain output in BED format since I wish to use `annotatr` finally which uses randomregions in ranges object form and I c…

annotatr regioneR gkmSVM

updated 5.0 years ago • rohitsatyam102

I am working with a non-model organism for which there are 2 versions of the genome. I would like to use the newer version as it has a better resolution and

DESeq2 Gnomon Biostrings

updated 4.8 years ago • sieminsk

et al., BMC Biol, 2013</span>).__ ### __We recently sequenced its genome and discovered its unique organization (____<span style="background-color:Yellow">Fang et al., Nat. Comm, 2014</span>). Further, differential gene expression

cancer BIOINFORMATICS genomics RNAseq miRseq Job

updated 10.8 years ago • aaron

I have a list of proteins (only `` Uniprot IDs ``) and I am interested in discovering relations between them. Most importantly I want to focus on disease pathways and find out whether the proteins I am looking at are part of particular disease(s). Additionally, functional relations, pathway analysis, simple category/class of protein, etc. can be helpful too. But disease pathways ar…

protein disease pathway analysis pathways

updated 7.4 years ago • ረ

Annotation GO Annotation GO

updated 13.8 years ago • Guido Hooiveld

TQ29\_STARhg19\_paired\_sorted.bam') > rnaseqgenes <- easyRNASeq(filesDirectory=getwd(), + organism='Hsapiens', + chr.sizes='auto', + readLength=100L, + annotationMethod='biomaRt', + format='bam', + count='genes', + summarization='geneModels...count=genes,summarization=geneModels deprecated paradigm. 2: In easyRNASeq(filesDirectory = getwd(), organism = …

easyrnaseq

updated 11.1 years ago • sylvian

txdb <- makeTxDbFromGFF(file="Homo_sapiens.GRCh38.90.gtf", format="gtf", dataSource="Ensembl", organism="Homo sapiens") allvar <- locateVariants(rd_abnorm, txdb, AllVariants()) # allvar is empty, no location annotation # GRanges

annotation variantannotation

updated 8.3 years ago • yduan004

sgrna_summary = path.sgRNASummary, proj = "Apr08", organism = "mmu" ) ``` It throws the error ``` Error in bmRequest(request = request, verbose = verbose) : Internal Server Error (HTTP 500). ``` When

software error

updated 5.7 years ago • alexch.liu

<div class="preformatted">Hi John, I am having trouble reproducing this. Can you please send me your "ilmn_cust_raw.txt" file along with the sessionInfo() when you built your package? Marc John Lande wrote: > dear All, > > I am trying to build an annotation package with annotationDbi. I followed > the instruction to build the package, with this script: &…

Annotation affy AnnotationDbi Annotation affy AnnotationDbi

updated 15.9 years ago • Marc Carlson

export(Celegans, "dataset/ce11.fasta", compress=FALSE) getGFF(db = "ensembl", organism = "Caenorhabditis elegans", reference = TRUE, path = file.path("dataset")) system("gunzip dataset/Caenorhabditis_elegans.WBcel235.91_ensembl.gff3.gz

systempiper edger rna-seq

updated 7.7 years ago • clarisbaby

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 probe oneChannelGUI Microarray Normalization probe oneChannelGUI

updated 15.3 years ago • rcaloger

<div class="preformatted">Of interest to those of you seeking gainful employment ----- Forwarded message from Giovanni Parmigiani <gp@jhu.edu> ----- Date: Thu, 06 Feb 2003 09:30:24 -0500 From: Giovanni Parmigiani <gp@jhu.edu> Subject: forwarded message from Mike West To: Giovanni Parmigiani <gp@jhu.edu> X-Mailer: VM 6.96 under Emacs 20.7.1 Date: Thu, 06 Feb 2003 07:59:4…

Genetics Cancer Breast Genetics Cancer Breast

updated 22.9 years ago • rgentleman

<div class="preformatted">Dear all, I'm analyzing a set of genes for GO enrichment, given a customized annotation. In that annotation, a specific GO term occurs only once; in my set of genes, the gene attached to it is also represented. I would have expected to find the numbers -- genes having a specific GO term in my list being "1" and genes having the term in total, in the annotation, b…

Annotation GO Organism GOstats Annotation GO Organism GOstats

updated 11.8 years ago • Christine Gläßer

1] "!Exptid=28370" [2] "!Experiment Name=hyperinsulinemic clamp in human muscle" [3] "!Organism=Homo sapiens" .....lots of lines.... For your information: I am using R V2.01, latest Bioconductor (updated yesterday) and marray

Microarray marray Microarray marray

updated 20.8 years ago • Rene Nederhand

m/f) to join our team. You will: - Lead the Core Facility Bioinformatics, coordinate and organize a team of bioinformaticians and IT specialists - Be responsible for long-term strategies for compute and storage

Epigenetics Infrastructure Epigenetics Infrastructure

updated 12.0 years ago • Holger Klein

baseName = myBase, baseMapType = myBaseType, pkgName = "hs95av2Refseq7", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = list(authors = "Weijun", maintainer = "Weijun <luo_weijun at="" yahoo.com="">"), fromWeb =T) here

Annotation probe annotate AnnBuilder Annotation probe annotate AnnBuilder

updated 19.5 years ago • Luo Weijun

file.path("gb.txt") > >> myBaseType <- "gb" > >> mySrcUrls <- getSrcUrl("all", organism="Rattus norvegicus") > >> myDir <- tempdir() > >> ABPkgBuilder(baseName=myBase, srcUrls=mySrcUrls, baseMapType...myBaseType, > >> pkgPath=myDir, organism="Rattus norvegicus", ... other …

Annotation GO Cancer r10kcod probe AnnBuilder PROcess biomaRt codelink Annotation GO

updated 18.8 years ago • Weiwei Shi

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 i…

Genetics Pathways Cancer PROcess microRNA a4 Genetics Pathways Cancer PROcess microRNA

updated 18.2 years ago • Prof. Roland Wagner

assembly_accession = "GCF_000841925.1", pkg_maintainer = "Jabez Battu <jabezbattu@gmail.com>", organism = "Helicoverpa zea Nudivirus-2", circ_seqs = "NC_004156.2", destdir = "E:/PhD data/RNAseq/TSS") ``` This ran succesfully showing

BSgenomeForge

updated 8 months ago • JABEZ RAJU

the vector as genelist. > -Used goProfiles package function basicProfile for this genelist with organism package of Arabidopsis. > > OUTPUT :Error in GOtermslist[[i]] : subscript out of bounds. > > Can somebody please help

GO Organism goProfiles GO Organism goProfiles

updated 12.4 years ago • Marc Carlson

The released packages include tools which facilitate: * annotation * data management and organization through the use of the S4 class structure * identification of differentially expressed genes and clustering

Normalization GO Cancer Normalization GO Cancer

updated 21.2 years ago • Jeff Gentry

biocViews = "AnnotationData", genomebuild = "S288C_reference_genome_R49-1-1_20051216", organism = "Yeast", manufacturer="Nimblegen", species = "Saccharomyces cerevisiae", url = "http://google.com") makePdInfoPackage(seed

BiocViews Annotation Organism biocViews BiocViews BiocViews Annotation Organism biocViews

updated 13.9 years ago • mabawsa

genomics data. The database engineer will be responsible for creating database solutions for data organization and management challenges in the department. Our team is responsible for thousands of patients worth of experimental

genomics analysis bioinformatics Job

updated 6.6 years ago • jmaanaki

the first bit of output: > g ================================== interaction entry ( 2009-11-25 ): ================================== [ organism ]: Arabidopsis thaliana Saccharomyces cerevisiae Schizosaccharomyces pombe [ taxonomy ID ]: 3702 4932 4896 [ interactors

GO Organism Arabidopsis thaliana graph RpsiXML GO Organism Arabidopsis thaliana graph

updated 16.1 years ago • Sara JC Gosline

read.flowSet it is not a vaild FCS2.0 or FCS3.0 file? These errors have me stumped. I think the organization of this library is quite keen. I like the flowFrame object in what I think of as a flowSet vector (with nice header

updated 18.6 years ago • M. Jankowski

populations are marked in a way that certain cells of similar origin based on the location in the organ have been differently marked where similar cells give rise to a secondary tumor while its adjacent region does not

deseq2 deseq

updated 9.3 years ago • vd4mmind

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

job Job

updated 6.6 years ago • rbrns

<div class="preformatted">Dear Jorge, I've Cc'ed the Bioc mailing list as it can be of help to others. You're missing the index (.bam.bai) files for your bam files; i.e. you need to run 'samtools index TTGR1.bam' on the command line in your /Users/jbeira/Desktop/bams directory to create the TTGR1.bam.bai file. You may as well want to use the indexBam function of the Rsamtools package. Th…

GO PROcess DESeq easyRNASeq GO PROcess DESeq easyRNASeq

updated 13.5 years ago • delhomme@embl.de

Hi, I am working with macaque, whose annotation and reference are not complete. I download Refseq annotation from UCSC and load the gtf using this. <pre> annotation_m = makeTxDbFromGFF(gtfFile, format = 'gtf', dataSource = 'ensemble', organism = 'Macaca fascicularis', …

GenomicFeature

updated 7.2 years ago • hxlei613

<div class="preformatted">Hi! Thank you a lot Benilton! The package works very nicely! I have analyzed my first HTA2.0 arrays without any problem! Best regards, Elena 2014-02-08 22:47 GMT+01:00 Benilton Carvalho <beniltoncarvalho@gmail.com>: > Hello, > > given the several requests I got re: supporting HTA 2.0 chips when using > oligo, I'm posting this m…

Annotation oligo pdInfoBuilder Annotation oligo pdInfoBuilder

updated 11.7 years ago • Elena Serrano