Bioconductor Forum

Normally one can use the inbuilt function to make a TranscriptDB from UNSC database however my organism, a plant, is not included in the UNSC database. Consequently I am trying to use the makeTranscriptDbFromGFF() function

Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures

updated 11.5 years ago • Guest User

nbsp;         jolma2013:    1 | 1 organism/s |           Hsapiens:    1 Hsapiens-jolma2013-ETV1 > lapply(ETVs

software error

updated 8.2 years ago • Ed Siefker

I understand that ReactomePA (suggested to be used from the ChIPseeker manual) does not support my organism (Lotus japonicus). But I do not how else I can make the Functional enrichment analysis of the ChIPseeker work. Could

ChIPseeker

updated 5.7 years ago • egbastakis

<div class="preformatted">To summarize our off-list discussion, and present our final suggested answer, using a sample entrez geneID to demonstrate, we offer the code shown below. A somewhat lengthy exposition of the 9 steps involved will be found below, following the 18 lines of excutable code. Thanks for posing this question, Eric, and for your patience while I worked up a reply. - Pa…

updated 12.5 years ago • Paul Shannon

Fernanda Costa [1]: https://genome.jgi.doe.gov/portal/pages/dynamicOrganismDownload.jsf?organism=Gmax

aspli readCounts rna-seq alternative splicing AS

updated 6.9 years ago • fernandalpcosta

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

software bioinformatics sequecing Job

updated 6.5 years ago • jmaanaki

<div class="preformatted">Hi Julian, The 1st thing to note is that you cannot actually produce a version 1.0 schema at this time. You can only make a 2.1 version schema. The older schemas are unsupported, and only the files remain for people who might encounter an older database. To answer your question about ACCNUM, this is a mapping that is normally used to store the ID that was origi…

BiocViews Genetics Annotation GO Organism probe biocViews AnnotationDbi BiocViews GO

updated 15.6 years ago • Marc Carlson

was aligned using RefSeq and then as DEXseq uses Ensembl I used a gtf/gff from Ensembl for the model organism I am working on. My code blocks that ran quite well with no error are placed below: ``` library(GenomicFeatures) download.file

DEXSeq HTSeq R

updated 2.4 years ago • yr542

technical and non-technical personnel in multiple fields of expertise and at various levels in the organization. - Knowledge of genetics, next-generation high-throughput sequencing, data security concepts and methods, Amazon

programming datascientist psychiatry bioinformatics JobPosting

updated 2.2 years ago • Belinda

an RNA seq dataset with EdgeR. I have 44 different samples, coming from two controls (both the full organ, namely a plant root) and five different cell types. I have 6 samples for all but one of the controls, for which I have 8 samples

edger

updated 8.5 years ago • elineverbon

siZ9_5312.bam"), + filesDirectory="/Volumes/Cellar/DNASeq_20121016/02.human/Orig_tophat _mapping", + organism="Hsapiens", + chr.sizes=as.list(seqlengths(Hsapiens)), + readLength=101L, + annotationMethod="rda", + annotationFile="./exon.annotation.biomart.rda

Annotation BSgenome BSgenome Annotation BSgenome BSgenome

updated 12.8 years ago • pepap

7.923474e-11 1 68 286 defense response to other organism BP</pre> So for example, __I want to know what those 135 genes are in the first category.__ To get the right gene mappings

goseq gene ontology biomart annotate category

updated 8.5 years ago • krc3004

Please be aware that the funds, as well as the space, for this event are limited, and the organizers need to balance the skills of the attendees, so not all qualified applicants can be guaranteed acceptance. The

Visualization Visualization

updated 18.3 years ago • Hilmar Lapp

GmbH provides consulting, services, and support to academic institutions and scientific research organizations. Scionics integrates information technology, data and image analysis techniques, and software development

job bioinformatics image analysis research software Job

updated 5.3 years ago • António Miguel de Jesus Domingues

Alignment Rattus norvegicus BSgenome BSgenome QuasR Alignment Rattus norvegicus BSgenome

updated 11.8 years ago • Guido Hooiveld

myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = myPkgName, pkgPath = myDir, organism = "Homo sapiens", version = "2.0.0", author = list(author = "Henrik Hornshoj <henrikh.jensen agrsci.dk="" at="">", maintainer = "Henrik

Genetics Annotation GO probe affy Genetics Annotation GO probe affy

updated 20.0 years ago • Henrik Hornshøj Jensen

etc. at the conference website: http://www.camda.info We look forward to seeing you in Berlin! The organizers and chairs of CAMDA 2013 12th International Conference on Critical Assessment of Massive Data Analysis Berlin

Genetics Classification Regression Genetics Classification Regression

updated 12.7 years ago • CAMDA 2013

invalid names for slots of class “GOHyperGResult”: pvalues, oddsRatios, expectedCounts, catToGeneId, organism Here the code I use: <pre> library( GO.db) library(org.Dr.eg.db) library (GOstats) pCutoff <- 0.05 params <- new("GOHyperGParams

gostats

updated 8.1 years ago • laianavarromartin

include tools which facilitate: 1. annotation (AnnBuilder, annotate). 2. data management and organization through the use of the S4 class structure (Biobase, marrayClasses). 3. identification of differentially expressed

Microarray Annotation Normalization Cancer genefilter geneplotter multtest ROC Microarray

updated 23.7 years ago • Anthony Rossini

<div class="preformatted">Hello, I just tried to get a probe to accession matching the above annotation database. In particular it does not yield any mappings for accessions. (i.e. x <- hugene10sttranscriptclusterACCNUM mapped_probes <- mappedkeys(x) yields an empty mapped_probes list. I'm Running R 3.1.1 on ubuntu. The loaded packages are: [1] oligo_1.28.2 Biostrings_2.3…

GO probe GO probe

updated 11.3 years ago • Thomas Pfau

names(gene_list))] #tried with and without removing duplicates kk <- gseKEGG(gene = gene_list_d, organism = "ko", keyType = "kegg", pvalueCutoff = 0.05, pAdjustMethod = "BH", seed=TRUE) sessionInfo( ) R version 4.3.2 (2023-10-31 ucrt) Platform

clusterProfiler gseKEGG

updated 21 months ago • andromeda

head(colData(se), 1) DataFrame with 1 row and 12 columns title geo_accession organism age sex infection <character> <character> <character> <character> <character> <character> GSM2545337 CNS_RNA-seq_11C

SummarizedExperiment

updated 15 months ago • Shuo GG

our Translational Science team. This team collaborates with the world’s leading biopharmaceutical organizations, utilizing Tempus’ data and platforms to deliver transformational impact across the entire drug development

JobPosting

updated 3.8 years ago • Ezgi

programming skills using R, Python, and Perl is a nice to have Demonstrated ability to organize, document and communicate scientific data Excellent verbal and written communication skills Ability to work

bioinformatics ngsReports NGS analyst science

updated 2.8 years ago • marisona.almazan

package Author: D.Y.Bilodeau Maintainer: D.Y.Bilodeau <danielle.bilodeau@ucdenver.edu> organism: Giardia lamblia common_name: Giardia provider: GiardiaDB provider_version: 35 release_date: 2017-08-15 release_name

cleanUpdTSeq BSgenome BSgenomeForge

updated 6.8 years ago • danielle.bilodeau

Institute of Biomolecular Science and Technology (LIBST) - in Louvain-la-Neuve **Context and organization** The Research logistician in bioinformatics will be based in the Louvain Institute of Biomolecular Science

transcriptomics proteomics job bioinformatician Job

updated 6.8 years ago • Laurent Gatto

Version: 0.1 License: Artistic-2.0 Author: Nicolas Mary Maintainer: Mary <nicolas.mary@envt.fr> organism: Apis mellifera genome: Amel-HAv3-1 common_name: Honey Bee provider: NCBI release_date: Sept. 2018 source_url: https

seedfiles BSgenome

updated 5.1 years ago • n.mary

stringsAsFactors=FALSE) samples <- sample_list[order(sample_list$Sample_ID),] #sort by ID to organize data #import counts from CountMerged.txt data from Step3-2 counts_file=("CountMerged.txt") counts <- read.table

edger differential expression rna-seq

updated 6.3 years ago • acs1990

object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: UCSC # Genome: mm10 # Organism: Mus musculus # Taxonomy ID: 10090 # UCSC Table: ensGene # UCSC Track: Ensembl Genes # Resource URL: http://genome.ucsc.edu

txdb genomicfeatures

updated 8.8 years ago • Chao-Jen Wong

University School of Medicine chromosome-level assembly of Astyanax_Mexicanus-2.0. Version: 1.4.2 organism: Astyanax mexicanus common_name: Cavefish provider: SIMR genome: astMex2NC release_date: April 2017 release_name

BSgenome

updated 4.7 years ago • Chris Seidel

amp;fq=regulates_closure:%22GO:0019083%22&sfq=document_category:%22annotation%22) - filter for Organism = human). I went to investigate further into org.Hs.eg.db using the select() function. library(org.Hs.eg.db) GO_virtcn

org.hs.eg.db

updated 7.4 years ago • katharina.baum

programming skills in R and/or Python - Independent and creative thinking - Very good work organization skills - Experience to work in interdisciplinary teams - Excellent communication skills in English **Additional

neuroscience data integration transcriptomics Job

updated 6.7 years ago • slezak

directory. >> count.table <- easyRNASeq(".", >> pattern=".sorted.bam$", >> organism="MMusculus", >> annotationMethod="gtf", >> annotationFile="mm9gene.gtf", >> count="genes", >> summarization...gt;>> count.table <- easyRNASeq(".", >>> pattern=".sorted.…

Transcription Sequencing miRNA SmallRNA Annotation Normalization GO Cancer Organism edgeR

updated 13.3 years ago • Weng Khong LIM

cluster/vyplab/first_weeks/recalled_nanopore/oarfish/', + source="localgencode", + organism="Homo sapiens", + release="42", + genome="GRCH38", + fasta=fastaFTP, + gtf=gtfPath, + write=FALSE, + jsonFile = "provaLinkedTxome.json

fishpond tximport tximeta

updated 11 months ago • brown.annaleigh

R, Python, and Perl Working experience in analysing large NGS datasets Demonstrated ability to organize, document and communicate scientific data Excellent verbal and written communication skills Ability to work

bioinformaticsspecialist ngsbasedassays statisticalmodels ngsdataanalysis differentialgeneexpression

updated 2.8 years ago • marisona.almazan

R, Python, and Perl Working experience in analysing large NGS datasets Demonstrated ability to organize, document and communicate scientific data Excellent verbal and written communication skills Ability to work

datascience bioinformatics ngsReports NGScopyData DataRepresentation

updated 2.8 years ago • marisona.almazan

sesameDataGet('MM285.mm10.manifest') mm10.txdb <- GenomicFeatures::makeTxDbFromEnsembl(organism = "Mus musculus", release = 102) seqlevelsStyle(mm10.txdb) <- "UCSC" txns.reproducible.example <- cdsByOverlaps(x = mm10.txdb

GenomicRanges sesame sesameData GenomicFeatures

updated 4.3 years ago • Pratik

I have RNA-seq data that I'm trying to run pathway analysis on. I'm using the GAGE R package. When I run the gage function, all the values are NA and I don't understand why. The only thing that I can think of is that my dataset does have some genes in it that are not in the reference gene set. This is because my organism was re-annotated by NCBI and I had to convert the new locus tags to old locu…

gage rna-seq pathwayanalysis

updated 5.2 years ago • microPhD

In installing and updating  bioconductor packages the dependency GO.db fails on widows on what looks like a parsing error brought about by a space in the path on E: drive.  I don't know if this is because the linux equivalent is "/e/program files/..." to the Windows "E:\\progem Files\\..." But, whether it is something else, but I'd be grateful for a workaround or better yet a f…

software error GO windows10

updated 8.8 years ago • Robert Baer

BSgenome object and a GRanges object. The BSgenome object contains the full genome sequences of the organism. The GRanges object contains the genomic ranges of your regions of interest. These can be the regions corresponding

Cancer BSgenome BSgenome IRanges Cancer BSgenome BSgenome IRanges

updated 11.4 years ago • Hervé Pagès

40784 keys) Additional Information about this package: DB schema: HUMAN_DB DB schema version: 1.0 Organism: Homo sapiens Date for NCBI data: 2009-Mar11 Date for GO data: 200903 Date for KEGG data: 2009-Mar10 Date for Golden Path

GO GO

updated 16.1 years ago • Vladimir Morozov

<div class="preformatted">Hi James, The current release and devel versions of Category have been patched. Barring any incident, these should now work more reliably and should also represent things more consistently internally. The latest versions of Category to look for are: 2.9.8 for devel and 2.8.2 for release. Thank you for reporting the bug. Marc James F. Reid wrote: > Dea…

Microarray Annotation Escherichia coli hgu95av2 Category Microarray Annotation hgu95av2

updated 17.1 years ago • Marc Carlson

analytics architecture and workflows for epidemiologic studies; establish data policies, standards, organization and enforcement of data governance; develop innovative approaches to link internal systems with external

bioinformatics Job

updated 9.2 years ago • kaufmanm

this means that I would have to store all matrixes (up to 10*6methods =60 matrixes) without further organization at the level of 'AssayData'. However, I'd like to keep at least one (in my case better 2) levels of additional arborescence

Annotation Annotation

updated 15.2 years ago • Wolfgang RAFFELSBERGER

nbsp; theme(legend.position="bottom") + geom\_text(aes(label=node)) but it only displays till "Organism".  Also tried adjusting margins with mar() and par(mai=c(2,0.82,0.82,6)) still no luck. Don't know how to go about getting

ggtree

updated 10.3 years ago • Alan Smith

Pathview not work with Bacillus subtilis subsp. subtilis 168 (=bsu) even though it's a KEGG organism? Or what am I doing wrong? I look forward to hearing from you. Sincerely yours, David </div

Microarray Annotation GO Bacillus subtilis gage pathview Microarray Annotation GO gage

updated 11.9 years ago • Luo Weijun

gt; I mean, in cross-species studies, or when comparing different tissues of >>> the same organism, if this assumption doesn't hold, should it be a serious >>> concern ? >>> >> >> In a cross-species comparison

Normalization Organism edgeR

updated 11.3 years ago • Gordon Smyth

to analyze GO terms associated with my DE genes. I'm trying to get the GO terms for my 'non-model organism' via the AnnotationHub. I'm trying to follow these instructions (given in the post https://support.bioconductor.org

edgeR limma annotationhub kegga annotationdbi

updated 9.5 years ago • Rinaldo Bertossa

We've just opened a position in the Division of Genetic Medicine at the Lausanne University Hospital (CHUV). This role will likely play a crucial part in our adoption of long-read sequencing (probably PacBio) in a clinical diagnostic setting: [https://recrutement.chuv.ch/vacancy/bio-informaticienne-chargee-de-recherche-311168.html][1] **Big plus if you are a Bioconductor contributor with experi…

GenomicRanges JobPosting

updated 5 weeks ago • story.benjamin

entire Illinois campus community, as well as off campus institutions, companies, and philanthropic organizations across the United States and around the world. The University of Illinois is an Equal Opportunity, Affirmative...160676) Open Date: 03/18/2022 Close Date: 04/15/2022 Organization Name: Metabolomics Center Apply for this…

Metabolomics

updated 3.8 years ago • Jenny Drnevich

sequence/strains/BY4742/BY4742_Toronto_2012/BY4742_Toronto_2012.gff.gz", dataSource="BY4742", organism="Saccharomyces cerevisiae") Import genomic features from the file as a GRanges object ... trying URL 'http://sgd-archive.yeastgenome.org

R VariantAnnotation

updated 3.3 years ago • rwan.work

<div class="preformatted"> Hi, I am using easyRNASeq for estimating the counts in an rna-seq alignment to hg19/GRCh37 done using bowtie2. I would like to get the counts "per gene". The code runs successfully and I get an output table, but the number of records in the output table are ~57000: cat count.tsv | wc -l 57774 I am wondering why the number of counts are so much greater than the …

GeneExpression RNASeq Genetics Coverage Normalization BSgenome Biobase Biostrings biomaRt

updated 11.7 years ago • Guest User

thinking, problem solving and analytical skills * You are a reliable team player with excellent organization and communication skills, and with a high degree of motivation   About Us Boehringer Ingelheim is a research

job Job

updated 10.1 years ago • holger.klein

gt; count_table <- easyRNASeq(getwd(), filenames = "Sample1.bam", + readLength = 52L, + organism = "Mmusculus", + chr.sizes <- seqlengths(Mmusculus), + format = "bam", + annotationMethod = "env", + annotationObject = exon_range

RNASeq Annotation Organism BSgenome BSgenome easyRNASeq RNASeq Annotation Organism

updated 13.3 years ago • Guest User

Parameters I used for enrichPathway(): down_204_pathway_enr <- enrichPathway(genelist, organism = "mouse", pvalueCutoff = 0.05) It ran. However, when I view the dataframe, it only shows me one dataframe head(as.data.frame

ReactomePA

updated 6.6 years ago • ayang

srcUrls= mySrcUrls, baseMapType = > mybasetype, pkgName = "monPackageAnnoted", pkgPath = mydir, organism = > "Homo sapiens", version = "1.0", author = list (authors = "Greg_Voisin, > Amelie Ouellet", maintainer = "voisingreg at yahoo.fr

annotate AnnBuilder annotate AnnBuilder

updated 18.7 years ago • Nianhua Li

new("NgsExpressionPDInfoPkgSeed", ndfFile = ndf, xysFile = xys, author = "", email = "", organism = "Mouse", species = "Mus musculus", url = "") makePdInfoPackage(pd.100718.mm9.exp, destDir = ".") install.packages("pd.100718.mm9.exp

pdinfobuilder oligo

updated 10.5 years ago • george.kararigas

Hi,I use GenomicFeatures to extract 5'UTR and 3'UTR and find that GenomicFeatures doesn't seem to regard stop codon as 3'UTR. I want to make sure about this and wonder how to change the raw R code to include stop codon. The following is my procedure. I download gencode V19 gtf file from gencode <https://www.gencodegenes.org/releases/19.html> (Comprehensive gene a…

genomicfeatures annotation utr

updated 7.5 years ago • hxlei613

<div class="preformatted">dear list and, particularly, dear domainsignatures package maintainers (Florian?), i was trying to use the package domainsignatures from the current BioC-devel version (see my sessionInfo at the end of this message) to test for the enrichment of a gene list throughout the collection of available KEGG pathways in mouse and found that the main function that collects…

Pathways Organism domainsignatures Pathways Organism domainsignatures

updated 16.1 years ago • Robert Castelo

_Unique.count.table <- easyRNASeq( filesDirectory = "./FruMA\_Male\_WCS\_Male/tophat\_BAM\_files/", organism = "Dmelanogaster", readLength=100L, chr.sizes = "auto", annotationMethod = "gtf", annotationFile = "Drosophila\_melanogaster.BDGP5.77.gtf...FruMA\_Male\_WCS\_Male/tophat\_BAM\_files/",        organism = "Dmelanogaster", readLe…

easyRNASeq

updated 10.6 years ago • surjray