Bioconductor Forum

Dear all, I am creating a local organism-specific version of uniproton on our server. Using the Bioconductor `Biostrings` package I experienced an "embedded

Biostrings

updated 6.4 years ago • daniel.magnus.bader

lt;-scan(genes,character()) Read 97 items > gs<-GSEABase::GeneSet(geneIds=inputGenes,organism='Homo Sapiens', + geneIdType=GSEABase::SymbolIdentifier()) > output<-teEnrichment(gs) Error in teEnrichment(gs) : could...lt;-scan(genes,character()) Read 97 items > gs<-GSEABase::GeneSet(geneIds=inputGenes,organism='Homo Sapiens', + …

TissueEnrich

updated 4.3 years ago • sarvesh.nikumbh

ago. So at the time I downloaded the ds_flat_ch*.flat files from here ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat in order to build SNPlocs.Hsapiens.dbSNP.20080617 (that was in March 2009), I assume that...these files were a dump from Build 129. Note that the files under ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/ASN1_flat can change at anytime (and today they are indee…

SNP Cancer SNPlocs SNP Cancer SNPlocs

updated 10.6 years ago • Hervé Pagès

I loaded by using Annotationhub, because my target species "acanthamoeba castellanii" is not a model organism. ``` hub <- AnnotationHub::AnnotationHub() amoeba <- query(hub, "Acanthamoeba castellanii") # title # AH65301 | Acanthamoeba...hub[["AH81410"]] > Acan.OrgDb OrgDb object: | DBSCHEMAVERSION: 2.1 | DBSCHE…

clusterprofiler GO

updated 5.7 years ago • Ruixuan

and multi- genome protein motif searches. ? Local establishment and customization of model organism genomic databases (e.g. ENSEMBL) and tools for batch sequence analysis utilizing these resources. ? Perform other...nearly $200 million annually in funding from government agencies, private groups and philanthropic organizations. Faculty members are nationally recognized authorities in a…

Genetics GO Cancer PROcess Genetics GO Cancer PROcess

updated 15.5 years ago • Julie Zhu

Invited sessions offer focused discussions on specialized topics. A prospective invited session organizer should send a proposal, including a session title, a short synopsis, bio-sketch of the organizer with a publication

updated 17.4 years ago • Linda Jones

Hi I'm working with non-model organism, doesn't have any information in the public domain. After denovo assembly using trinity for all 32 samples, using...Hi I'm working with non-model organism, doesn't have any information in the public domain. After denovo assembly using trinity for all 32 samples, using salmon...Now, how do i create, tx2gene dataframe, the genome,GTF information is not a…

tximport

updated 5.7 years ago • sunnykevin97

genes <- data$Ensembl_Gene_ID genes <- as.character(genes) ggo <- groupGO(gene = genes, organism = "human", ont = "BP", level = 3, readable = TRUE) # Enrich GO genes<-data$Ensembl_Gene_ID[abs(data$log2FC_DeSeq)>2] ego <- enrichGO...genes , organism= "human", ont= "CC", pAdjustMethod="BH", pvalueCutoff=0.1, qvalueCutoff=0.5, readab…

clusterprofiler input files error help

updated 9.0 years ago • Mataivic

AnnBuilder"), "data", "thgu95a") > myBaseType <- "gb" > mySrcUrls <- getSrcUrl("all", organism = "Homo sapiens") > mySrcUrls LL "ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz" GP "http://hgdownload.cse.ucsc.edu...mySrcUrls, baseMapType = g, + pkgName = "myPkg", + pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", + …

Cancer Organism AnnBuilder Cancer Organism AnnBuilder

updated 21.3 years ago • Richard Friedman

Im a beginner in R and I want to forge Casuarina equistifolia genome in BSgenome package as it is not available as inbuilt package. After spending so much time in solving errors but still I couldn't solve one error. Kindly help me to solve the below error. #Seed File I have used ``` Package: BSgenome.Cequisetifolia.NCBI.ASM379533v1 Title: Full genome sequences for Casuarina equisetifolia incan…

BSgenome.Cequisetifolia.NCBI

updated 3.5 years ago • Manoj Kumar R

genome = gen, chromosome = chr) #TxDb object txdb <- makeTxDbFromGFF(file="assembled.gtf", organism="Homo sapiens", format = "gtf") #gene track grtrack <- GeneRegionTrack(txdb, genome = gen, chromosome = chr, fill='black', transcriptAnnotation

Coverage RNASeq plot Gviz

updated 4.6 years ago • karlaarz

clustering clusterprofiler

updated 9.4 years ago • zhangducsu

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 19.3 years ago • Sturgill, David NIH/NIDDK [C]

power curve. I have a good number of samples (__85__), coming from 3 different organs, each at different developpement stages (5 replicates per stage). A mass spectrometry was performed, giving a spectral

wgcna picksoftthreshold scale-free topology co-expression network

updated 7.9 years ago • marcantoine.guery

modeling of gene network and embryonic development evolution.   c. Mathematical modeling of organ development and their evolution in mammalian teeth or Drosophila wing.   The actual project will be chosen together...nbsp; The job is for 1 year and renewable for 1 extra year.   2. Background:   Why organisms are the way they are?   Can we und…

job computational biology simulation evolution Gene network Job

updated 8.6 years ago • isaac.salazar

gt; #save in a TSV format (the file is saved in txt) >>> write.table(tmpgene,"Z:/**tomhait/organisms/human/** >>> transcript_names.txt", >>> row.names=FALSE, quote=FALSE) >>> #collect all sequences with upstream...as.character(transcript_**flank))) >>> >>> #writing to a ne…

Network biomaRt Network biomaRt

updated 13.4 years ago • Stefan Kroeger

chr",c(1:19,"X","Y"),sep=""),2)) 2) rerun you command with the chr.map argument and a "custom" organism argument rnaSeq2 <- easyRNASeq(filesDirectory=extdataDir, organism="custom", chr.sizes=chr.sizes, filter=myfilt...validity.check=FALSE in the easyRNASeq command rnaSeq2 <- easyRNASeq(filesDirectory=extdataDir, …

Sequencing Alignment Annotation Organism BSgenome biomaRt BSgenome easyRNASeq Sequencing

updated 14.0 years ago • delhomme@embl.de

am getting similar errors stating that there is no genome assembly fasta file available for these organisms. I tried with multiple versions of the AnnotationHub EnsDb object for each species and continue to get the same...snapshotDate(): 2022-10-31 Error in .local(x, ...) : No genome assembly fasta file available for organism: Xenopus tropicalis, data provider: Ensembl and genome version: Xeno…

AnnotationHubSoftware ensembldb

updated 2.4 years ago • cjag

Code: > avn <- pathview(gene.data=pathview_genelist, pathway.id="avn01200", species = organism) > avn <- pathview(gene.data=gene_list, pathway.id="avn01200", species = organism, kegg.native = F) Error: > Note: Mapping

KEGGREST pathview R

updated 2.9 years ago • morgan.sobol

and data consulting company based in The Hague, the Netherlands. We build serious tools to help organizations turn data into information, and information into results. Our clients include humanitarian relief organizations

job renjin reseach Job

updated 10.7 years ago • mj

Ingelheim Foundation is recruiting a Post-Doctoral Fellow in Bioinformatics Proteome organization and dynamics (#AKPD02) The Institute of Molecular Biology (IMB) is a Centre of Excellence for Life Sciences located...Experience with mining and integration of large data sets with R and Python • Very good work organization skills and the ability to work independently • Work experience in…

Job Advert

updated 6.3 years ago • l.brown

I apologise if some version of this question has already been asked in some way- I could not find any issues that were similar to my own. I have a choice between taking data from the datasource package 'MotifDb' and 'JASPAR2018': MotifDb has a much larger wealth of data: <pre> library (MotifDb) library("BSgenome.Mmusculus.UCSC.mm9") tf_motif_hoco=subset(MotifDb, organism=='Mmusculus')…

pwm pfm jaspar motifdb

updated 7.1 years ago • chrisclarkson100

KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware

updated 22 months ago • fernanda.backsouza

The [Community Advisory Board][1] (established in 2020) is seeking nominations from new members. If you're interested in becoming more involved in the Bioconductor project in the area of community building (e.g. conference and meet-up organization / helping new users / promoting Bioconductor via social media etc.), then please consider applying to the join the...involved in the Bioconductor proj…

Bioconductor CAB bioconductoroversight community

updated 3.1 years ago • shepherl

had to add a pseudocount in order for it to run). The results were the following (I faceted them by organ to be "cleaner" to see any possible pattern in other subgroups): ![PCA Results][1] However, when performing DE in the full dataset

DESeq2 RNASeq

updated 3.0 years ago • andrebolerbarros

https://rdrr.io/cran/biomartr/man/getGFFSet.html library(biomartr) getGFFSet("refseq", organisms = c("Arabidopsis thaliana", "Arabidopsis lyrata", "Capsella rubella")) Running it online results in the following: Starting

getGFF NCBI biomartr biomaRt

updated 4.5 years ago • Matan G.

Hello, Bioconductor, I'm working lately with data from small-RNA seq in an organism without small RNA annotation. I would like to perform DE analysis on Differentially Expresed Regions and I would

derfinder

updated 4.6 years ago • Konstantinos Yeles

the following: library(KEGGgraph) tmp <- tempfile() retrieveKGML(pathwayid='mmu04015' , organism='mmu' , destfile=tmp, method="wget") pathway <- parseKGML(tmp) nodes\[\[60\]\]@name\[\[1\]\] ---> retrieves mmu:12801 nodes\[\[60\]\]@name\[\[1\]\] ---> retrieves

kegggraph

updated 10.1 years ago • Osvaldo

<span style="font-size:13px; line-height:1.6">I am performing an analysis of targeted proteomics for a study with rather sophisticated study design.  As a result of this and other issues (like novelty of the data itself) I found myself writing a lot of custom code  (such as visualization, normalization, etc.).  The code just begs to organize itself into a package.…

package guidelines

updated 11.1 years ago • petyuk

Hello everyone, I have a little bit confused in using biomaRt. I would like to retrieve GO term definition and name for each GO ID. I have done following mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "asia.ensembl.org") go_list <- getBM(attributes=c("go_id", "name_1006", "namespace_1003"), filters = "…

biomaRt GO term

updated 6.7 years ago • Taiki Tsutsui

up calculations I offer advice that they should download a copy of the KGML directory for their organism to their local machine, and I want the package to know where those files are at runtime. Thanks in advance, -Robert Robert

Organism Organism

updated 15.3 years ago • Robert M. Flight

on R? Is there another easier way to load all the data at once? -> What is the better way to organize the data to compare the samples coming from the patients infected with bacteria 1 and 2? Bacteria 1 20180202 LA 02

proteomics LC-MS/MS

updated 6.9 years ago • pdaltron

Hi, I am attempting to do a differential expression analysis comparing one organism supplemented with bacteria and another that is not. When looking at my MA Plot it appears that there are man genes

deseq2 rna-seq

updated 10.7 years ago • ejmcmaho

at the moment, but I use getBM in a loop over several marts because I need sequences of several organisms. Strangely, in the loop it works even fewer times. Currently I'm on host 'useast.ensembl.org', I've tried 'www.ensembl.org

biomaRt getBM

updated 5.9 years ago • laurenz.holcik

<div class="preformatted">Hi , I'm a bit confused in the way of using my data. My input is a list of genes( in fact a list of targeted genes for microRNAs). The first step is to get the GoTerms associated to these genes and then i would like to do hyperg to obtain significant dysregulated Goterms. ALl the examples i went through use affy data or so so i'm not sure this is correct. I would …

Organism affy Organism affy

updated 14.9 years ago • David

columns of result is not a multiple of vector length (arg 1) 2: In easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes, : There are 229182 features/exons defined in your annotation that overlap! This implies...be counted more than once! Is that really what you want? 3: In easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes, : You e…

RNASeq Annotation Normalization Cancer Organism BSgenome BSgenome easyRNASeq RNASeq

updated 13.2 years ago • Richard Friedman

Hi, I'm trying to run create an annotation database for Agaricus bisporus through NCBI in AnnotationForge, but I get a couple of errors: Error in makeOrgDbFromDataFrames(data, tax\_id, genus, species, dbFileName,  :   'goTable' GO Ids must be formatted like 'GO:XXXXXXX' In addition: Warning messages: 1: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI…

annotation microarray annotate annotationforge

updated 9.0 years ago • MOD

new_pages/submission/sub_papers.html Workshops & Tutorials: Submit a proposal to organize one! ---------------------------------------------------------------------- ---- The conference will begin with a day of workshops and tutorials: two full-day workshops and four half-day tutorials

updated 20.0 years ago • Hershel Safer

baseMapType = "ll",pkgName="Hum30kbatch1to5", pkgPath="C:/Installerade program/R/tempdir/hum", organism = "human", version = "1.1.0", makeXML = TRUE, author = list(author = "Johan Lindberg", maintainer = "johanl@biotech.kth.se"), fromWeb

Annotation Organism Annotation Organism

updated 21.3 years ago • Johan Lindberg

is to identify mRNAs that are bound to one translational factor (compared to another factor) 2) Our organism has 8,000 genes 3) We use a modified RNAseq where each read represents one mRNA transcript. 4) and our library usually

RNASeq Organism edgeR RNASeq Organism edgeR

updated 13.8 years ago • gowtham

data.frame(frame$go_id, frame$Evidence, frame$systematic_name) goFrame <- GOFrame(goframeData, organism = "Saccharomyces cerevisiae") goAllFrame <- GOAllFrame(goFrame) Sc.gsc <- GeneSetCollection(goAllFrame, setType

gostats

updated 11.0 years ago • nonCodingGene

to a certain way of gene expression testing between sample groups) - Is available for a number of organisms and gene set annotations (at least GO and KEGG) - Allows one to ignore the direction of the regulation and concentrate

GO GO

updated 14.9 years ago • Asta Laiho

to depend on other databases (e.g. miRbase) which are not very useful for more recently sequenced organisms where all we usually have is a fasta sequence file and a gff/gtf annotation file<span style="line-height:1.6">. Since

GenomicFeatures rtracklayer

updated 10.9 years ago • Thomas Girke

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

Network oneChannelGUI Network oneChannelGUI

updated 13.1 years ago • raffaele calogero

5 technical replicates (100 samples thus) The first two time points are really early is the organism's life cycle and hence we often expect less reads for some genes: After summing the reads from the technical replicates

deseq2

updated 7.5 years ago • xei6

I am using the enricher function of clusterprofiler for GO enrichment of my non-model organism. First I have my DE genes (n=638, converted as character): gene <- read.csv("list.csv", header = F,sep=",") gene <- as.character

software error go annotation clusterProfiler

updated 5.9 years ago • tianshenbio

awk '($7 == "=")' > output.sam, then it can run. ```r txdb<-makeTxDbFromEnsembl(organism="Homo sapiens", release=103, circ_seqs=NULL, server="ensembldb.ensembl.org", username="anonymous", password=NULL, port

ASpli

updated 4.9 years ago • stephen66

is.na(gc$entrezgene_id))] #entrez genes existant pour l'humain ens=gprofiler2::gconvert(genes, organism="hsapiens", target='ENTREZGENE_ACC')$target #entrez gene de nos genes ensint=factor(as.integer(ensfull %in% ens))#preparation

topGO devtools R

updated 5.6 years ago • emisecherre

are revolutionizing genetics by allowing us to sequence the genomes of many different individual organisms in a population and to observe their complex coding and non-coding transcriptomes and regulatory events under

Sequencing Genetics genomes Sequencing Genetics genomes

updated 16.2 years ago • Wolfgang Huber

Selected post-doctoral candidates will join a dynamic oncology drug discovery and development organization to study therapeutics that treats cancer. Candidates will have the opportunity to collaborate across the...Ingenuity) and internal sources in analyses. Candidates will work independently as part of a matrix organization. Candidates will communicate Bioinformatics results to computational bio…

Job

updated 11.1 years ago • Michael Gormley

<div class="preformatted">After converting my custom gene2Domains mapping into a list of vectors > head(entrez2interpro_nested) $`679594` [1] "IPR019956" "IPR019954" "IPR019955" "IPR000626" $`682397` [1] "IPR019956" "IPR019954" and feeding that into retrain(), I now have the 4th model (most complete?), built using genes: 5667 of 5667 features: 4007 level detectors: 78 This obsol…

Genetics Coverage biomaRt gene2pathway Genetics Coverage biomaRt gene2pathway

updated 15.5 years ago • Bogdan

genome as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects. Version: 1.0 organism: Cicer arietinum species: Chickpea provider: NCBI provider\_version: ASM33114v1 release\_date: Jan. 2013 release...Shenzhen ASM33114v1 source\_url: https://www.ncbi.nlm.nih.gov/assembly/GCF\_000331145.1/\#/def organism\_biocview: Cicer\_arietinum BSgenomeObjname…

bsgenome bsgenome forge

updated 8.6 years ago • jodiera

I would like to use `ggbio` for *C elegans* and am [following along with this tutorial for biovizBase][1]. When adding a **gene model track** the code looks like this: ``` library(ggbio) library(Homo.sapiens) #load gene symbol : GRanges, one gene/row data(genesymbol, package = "biovizBase") ``` Looking at the help for `?genesymbol` it looks like this is a dataset for humans. The pac…

biovizBase ggbio

updated 5.9 years ago • moldach

I used the latest database, but the data obtained than the old database, the lack of exactly what I want. As follows, I use the "AnnotationHub(), query(hub,'zea') " function to get the results shown in the left, but I get the result is the right look, the lack of 'AH55736' is exactly what I want. ![](http://img.blog.csdn.net/20170811091923787) Then I try to change the "snapshotDate()" da…

orgdb annotationhub

updated 8.6 years ago • slbai01

I'm trying to use clusterProfiler to perform gene set enrichment analysis. My differentially-expressed gene dataset has Ensembl IDs in addition to log2foldChange values. First I ran the following chunk of code, and returned a "no term enriched under specific pvalueCutoff" error: ``` > gse_hfd <- gseGO(geneList = hfd_gene_list, ont = "ALL", keyType = "ENSEMBL", minGSSize = 3…

AnnotationDbi GO clusterProfiler enrichplot ensembldb

updated 3.4 years ago • simone.nevills

**OUR COMPANY** At Boehringer Ingelheim we develop breakthrough therapies and innovative healthcare solutions in areas of unmet medical need for both humans and animals. As a family owned company, we focus on long-term performance. We believe that, if we have talented and ambitious people who are passionate about innovation, there is no limit to what we can achieve; after all, we started with …

R/Bioconductor Job

updated 5.5 years ago • nico.komarowsky.ext

enrichResult (71.9 MB). If if look into it: > edo # # over-representation test # #...@organism Homo sapiens #...@ontology DisGeNET #...@keytype ENTREZID #...@gene chr [1:1018] "49855" "9880" "8879" "11260" "1292" "55039" "3908" "85415" "10519

enrichplot

updated 4.4 years ago • Pahi

zmays_eg_gene dataset from genome annotation version of the plant_mart mart. biomartr::organismBM(organism = "zea mays") #We retrieve attributes from zmays_eg_gene for Zea mays zea_attributes <- biomartr::organismAttributes

biomaRt clusterProfiler Zea_mays

updated 2.1 years ago • sanchezsanchez

made a separate set that is just my intensities. In this case, we are looking at a mutant vs wt organism for differential protein expression. These both have 4 replicates. Once my data was filtered and I made a df (1014x18

Proteomics limma vsn

updated 4.5 years ago • Chris

Hello,  I have been trying to reproduce results from gsea using clusterprofiler and gseKEGG (for some unknow reason gseGO is not working for me ) simply repeating experiment on the same gene expression data about 13k genes:   gseKEGG(geneList = zscores,                 &…

gsea clusterprofiler

updated 8.1 years ago • Stane