Bioconductor Forum

URGI; v1a) see https://urgi.versailles.inra.fr/Species/Pisum/Pea-Genome-project Version: 1a organism: Pisum sativum common_name: Pea genome: Pisum_sativum_v1a provider: URGI provider_version: Pisum_sativum_v1a

BSgenome

updated 5.0 years ago • sophie.harrington

kgml.path="C:\\Users\\David\\Documents\\R\\win-library\\3 .0\\SPIA\\extdata\\keggxml\\hsa",organism="aag",out.path="C:\\Users\\D avid\\Documents\\R\\win-library\\SPIA\\extdata\\") This resulted in [1] TRUE and an aagSPIA.RData file

SPIA SPIA

updated 12.0 years ago • David Price

sequences for Zea mays (AGPv3) Description: Full genome sequences for Zea mays Version: 1.0.0 organism: Zea mays common_name: maize provider: NCBI provider_version: release_date: Oct. 2015 release_name: MaizeGDB source_url

bsgnome forge

updated 10.3 years ago • Marcin Grzybowski

<div class="preformatted">Dear all, Now I am using pathview to map my RNAseq expression data to the keggmap of my organism 'mez'. I want to know how pathview deal with the colour of enzyme with several conding genes, for example: In pathway: Glycolysis...Dear all, Now I am using pathview to map my RNAseq expression data to the keggmap of my organism 'mez'. I want to know how pathview dea…

RNASeq Organism pathview RNASeq Organism pathview

updated 11.9 years ago • 刘鹏飞

GOSemSim package, but I am getting the following error:   __> mgeneSim(protein\_id\_list, organism="human")__     <0 x 0 matrix>     There were 50 or more warnings (use warnings() to see the first 50) __> warnings

GOSemSim mgeneSim

updated 9.7 years ago • ረ

## __New: Master of Science (Laurea Magistrale) in Quantitative and Computational Biology__ ### ___University of Trento, Italy___ a __multidisciplinary degree that formally integrates quantitative sciences and applied biology__, thanks to the following organizations at the University of Trento: * <a href="http://www.cibio.unitn.it/" target="_blank">CIBIO, Centre for integrativ…

computational biology bioinformatics teaching master News

updated 9.5 years ago • enridomenici

<div class="preformatted">Dear Bioconductor Developers and Users, I have created few annotation packages which are for organism specific proteomics database from IPI(http://www.ebi.ac.uk/IPI/IPIhelp.html) . Now I am keen on writing a generic utility...Dear Bioconductor Developers and Users, I have created few annotation packages which are for organism specific proteomics database from…

Microarray Proteomics Annotation GO Microarray Proteomics Annotation GO

updated 18.2 years ago • Chanchal Kumar

<div class="preformatted">Hi all, actually, I have (a) similar question(s) regarding a very non- standard Agilent data set: this is a custom 60mer oligo chip, the probes of which are designed from Arabidopsis thaliana sequence information, but intended to measure expression in the related non-model organism Arabis alpina. There are several probes per A. thaliana gene (not always the same…

Organism Arabidopsis thaliana probe affy oligo Organism Arabidopsis thaliana probe affy

updated 17.8 years ago • Ulrike Goebel

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 15.8 years ago • Wolfgang Huber

gt; ABPkgBuilder(baseName=myBase,srcUrls=mySrcUrls,baseMapType="ll", + pkgName="rats",pkgPath=myDir,organism="Rattus norvegicus",version="1.1.0", + author=list(authors="Alice",maintainer="alice.johnstone at esr.cri.nz"),fro mWeb...baseName = myBase, srcUrls = mySrcUrls, baseMapType = "ll", pkgName = "rats", pkgPath = myDir, organism = "Rattus norvegicus", version = "1.1.0", author =…

Annotation Organism Annotation Organism

updated 18.1 years ago • Johnstone, Alice

Hi everyone, I have problem in reproducing vignette example from MeSHDbi package. That is, when I run: <pre> > example("makeGeneMeSHPackage")</pre> It should use  preformatted data frames "PAO1" and "metaPAO1" to construct custom org.MeSH.XXX.db package that can subsequently be loaded via library() and queried with Annotation.dbi or RSQLite, or at least that is ho…

annotation annotationdbi rsqlite

updated 10.8 years ago • Ceca Bojic

249") # Pathway enrichment analysis enriched_pathways <- enrichPathway(gene = random_genes, organism = "mouse") # Extract pathway and gene information pathways <- as.data.frame(enriched_pathways) `# Create an edge list

EnrichedPathways GeneInteractionGraph graph

updated 18 months ago • Antonio

0.01, qvalueCutoff = 0.05) ``` returning: ``` # # over-representation test # #...@organism Homo sapiens #...@ontology BP #...@keytype SYMBOL #...@gene chr [1:294] "SORBS1" "PIK3C3" "TBC1D4" "SKP2" "PELI1" "SCIN" "LPL" "SPOPL" "BRAF" "SIRT1

clusterProfiler enrichGO

updated 4.1 years ago • samsiljee

indexDir = "/Users/atari/biodata/genomes/ensembl_hg38/indexes/SALMON", source = "ensembl", organism = "Homo Sapiens", release = 98, genome = "GRCh38", fasta = "/Users/atari/biodata/genomes/ensembl_hg38/transcripts/ensembl_hg38_transcripts.fa.gz

tximeta

updated 4.1 years ago • atariw

have done RNAseq and the usual differential gene expression analysis pipelines (Deseq, etc) in one organism under two different conditions and now, we would like to do it between these different bacteria. We have 2 different

DEG RNASeqData DifferentialExpression SCBN RNASeq

updated 22 months ago • Abril

Homo sapiens BSgenome BSgenome Homo sapiens BSgenome BSgenome

updated 11.5 years ago • Asma rabe

Loading required package: RCurl Loading required package: bitops extracting only data for our organism from : gene2pubmed Getting data for gene2accession.gz Error in sqliteSendQuery(con, statement, bind.data) :&nbsp

annotation annotationforge annotationdbi makeorgpackagefromncbi

updated 10.9 years ago • oliver.tills

txdb TxDb object: # Db type: TxDb # Supporting package: GenomicFeatures # Data source: BioMart # Organism: Saccharomyces cerevisiae # Taxonomy ID: 4932 # Resource URL: www.biomart.org:80 # BioMart database: ensembl # BioMart

makeTxDbFromBiomart genomicfeatures txdb biomart

updated 10.2 years ago • vinod.acear

from well-controlled experiments are 0.4 for human data, 0.1 for data on genetically identical model organisms or 0.01 for technical replicates. " But I came across this post which mentions a conservative way to calculate BCV

edgeR edgeR

updated 12.0 years ago • Bade

clusterProfiler) > data(gcSample) > xx <- compareCluster(gcSample, fun="enrichKEGG", + organism="hsa", pvalueCutoff=0.05) > p1 <- emapplot(xx) Fehler in (function (classes, fdef, mtable) : unable to find an inherited method

emapplot enrichplot clusterProfiler compareCluster

updated 5.9 years ago • rapmic

<div class="preformatted">I regret that I must announce the cancellation of the course announced below, owing to logistic difficulties and low turnout for this particular date. When the course is rescheduled, it will be announced on this list. On Tue, Sep 17, 2013 at 1:10 AM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > This two day course is described in a preliminary…

Annotation Annotation

updated 12.3 years ago • Vincent J. Carey, Jr.

Hi all,  I was just wondering if somebody could help me regarding normalized count after DESeq. I carry out a DESeq on a time course experiment in order to then make a count matrix of significantly expressed genes to look for patterns in gene expression across different samples. However, I have noticed that the count matrix I am making post DESeq on significantly expressed genes are ac…

DESeq2 results

updated 7.7 years ago • A

bioconductor annotationdata hgu133a

updated 7.8 years ago • Agaz Hussain Wani

2, ..., 10 (total: 10) geneIdType: Null collectionType: Null setIdentifier: MyId description: organism: pubMedIds: urls: contributor: setVersion: 0.0.1 creationDate: > c(setName(myGset), setIdentifier(myGset)) ; [1] "MyName...Null setIdentifier: bdmgWorkstation2:28927:Tue Jan 24 12:09:13 2017:1 description: organism: pubMedIds: urls: contributor: …

software error bug gseabase

updated 8.9 years ago • jcrodriguez

of FC values in each condition separately. <pre> > viewPathway("Scavenging by Class B Receptors", organism = "human", readable = TRUE, foldChange = cond1FC, vertex.label.font = 3, vertex.label.cex = 0.7, col.bin = 10, legend.x = 1, legend.y...columns</pre> http://imgur.com/w77zQO4 <pre> > viewPathway("Scavenging by Class B Receptors", organism = "human", reada…

DOSE ReactomePA

updated 9.0 years ago • Kajus Baidžajevas

notes)) { cat("Generating notes from ", fnames[1], "\n", sep="") row <- grep("Organism", y)[1] organism <- strsplit(y[row], "=")[[1]][2] row <- grep("Category", y)[1] category <- strsplit(y[row], "=")[[1]][2] row <- grep("Subcategory", y)[1] subcategory...collapse = ",") else parameter…

Cancer Breast Organism probe Category Cancer Breast Organism probe Category

updated 21.6 years ago • Mayte Suarez-Farinas

REVIGO website for some reason, I've been trying to use rrvgo package. I'm working with a non-model organism, so I used Blast2GO to annotate the sequences and obtain their associated GO terms. Also, I created an OrgDbPackage

AnnotationHub GOSemSim rrvgo

updated 14 months ago • daccar98

Hsapiens, chrs="chr21", width=250, spacing=250) > cpgdens <- cpgDensityCalc(windows, organism=Hsapiens, w.function="linear", window=700)   > sI <- matrix(rnbinom(2\*length(windows), mu=5, size=2), ncol=2) > bm <- BayMethList

repitools

updated 10.4 years ago • Matthias Lienhard

and that you provide me the list of exon level probe sets you are trying to plot and which organism you are using. Cheers Raffaele -- ---------------------------------------- Prof. Raffaele A. Calogero Bioinformatics and Genomics Unit Dipartimento di Scienze

Organism probe oneChannelGUI Organism probe oneChannelGUI

updated 16.5 years ago • raffaele calogero

<div class="preformatted"> Call for Contributions ===================================================================== LIFE SCIENCE FREE SOFTWARE SESSION held at CompLife 2006 (http://www.complife.org) in Cambridge, United Kingdom, on September 27 - 29, 2006 ===================================================================== In the l…

updated 19.6 years ago • Thorsten Meinl

Hi Bioconductor Support, Since 2018 I've been interacting with rOpenSci's organizers. For those that don't know, [rOpenSci](https://ropensci.org/) is a non-profit that aims to > make scientific data retrieval

ropensci webinar News

updated 5.8 years ago • Leonardo Collado Torres

<div class="preformatted">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.package=TRUE, remove.duplicates=FALSE, use.bagging=TRUE, nbag=11) Retrieving KEGG information...gt; retrain(minnmap=30, level1Only="Met…

updated 16.1 years ago • Dick Beyer

but the result is in line with the current knowledge of sex-biased gene expression in my model organism. I have done some quality control plots, available here: - Boxplot: http://www.iee.uu.se/zooekol/pdf/hemiarray_qc_boxplot.pdf

Normalization affy limma Normalization affy limma

updated 16.7 years ago • Paolo Innocenti

step is for CEOs and other business leaders to recognize the strategic role that IT plays within an organization. We all know and love normal radio. uk - Save Internet Radio. </div

PROcess PROcess

updated 18.5 years ago • Charlie

<div class="preformatted">Hi, Hope you're fine I am trying to make whole genome plots using the geneplotter package/annotate package. The organism I am studying is Arabidopsis thaliana, and obviously the annotations are not so extensive there: when trying to build...re fine I am trying to make whole genome plots using the geneplotter package/annotate package. The organism I am studying i…

Organism ath1121501 Organism ath1121501

updated 17.2 years ago • Samuel Wuest

<div class="preformatted"> Hi, I have a question regarding the minimal number of genes that we can test in an analysis with edgeR. Let me explain, in a study, edgeR have been used for testing the differential expression of three viruses between two conditions, without considering the counts on other features. That is, the data frame d$counts has only three lines (and 4 columns, as there i…

Organism edgeR Organism edgeR

updated 13.2 years ago • Guest User

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 easyRNASeq Coverage GO

updated 12.1 years ago • Nicolas Delhomme

looks great. Would that we had such a resource (curated, > current, and growing) for all organisms! > > A few questions, if I may: > > 1) What role with respect to FlyFactorSurvey do you picture us taking here > at...policy? > > 4) Is TRANSFAC only for license holders? > > 5) Are there any other organism-speci…

Annotation GO MotIV Annotation GO MotIV

updated 13.7 years ago • Vince Schulz

to study the functional (expression) evolution of mammalian genomes across gene types, lineages, organs, cell types, developmental stages, chromosomes and sexes. The postdoctoral fellow will be funded by a recently awarded...R., Paabo, S., and Kaessmann, H. (2011) The evolution of gene expression levels in mammalian organs. Nature 478: 343-348. &nbsp

rnaseq genomics evolution Job

updated 9.8 years ago • henrik.kaessmann

myBaseType, + + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, Error: syntax error > + organism = "Homo sapiens", version = "1.1.0", makeXML = FALSE, Error: syntax error > + author = list(author = "myname", maintainer = "myname at...mySrcUrls, baseMapType = myBaseType, + otherSrc = myOtherSrc, pkgName = "myPkg", pkgPath = myDir, + organism = "Homo sapiens", version = "1.…

GO Organism AnnBuilder GO Organism AnnBuilder

updated 20.0 years ago • Yong Jiang

I have some general questions about doing a time series RNA-seq experiment. The RNA is from a non-model organism. The experiment has no conditions for comparison (so just the "control" condition, essentially). Three biological replicates...some general questions about doing a time series RNA-seq experiment. The RNA is from a non-model organism. The experiment has no conditions for compariso…

DESeq2

updated 3.0 years ago • Dunois

# Group Greeting Cards in R Are you looking for a fun and personalized way to celebrate a special occasion with a group of friends, family, or colleagues? Group greeting cards in R might be the perfect solution! With R's powerful data manipulation and visualization capabilities, you can create custom greeting cards that include messages and images from multiple contributors. Here's how it w…

CARNIVAL

updated 2.4 years ago • carterethan745

Genomics Research (CGR) laboratory in Gaithersburg, MD, is an advanced, fast-paced, high-throughput organization dedicated to the support of molecular, genetic and epidemiologic studies for investigators at the National

bioinformatics

updated 2.9 years ago • Wendy

Hello! I have a list of about 6400 differentially expressed genes and I want to perform KEGG pathways enrichment analysis using the clusterProfiler package. I first did it with the ORA method, using the `enrichKEGG` function and doing it separately on the genes with positive and negative logFC. I got hundreds of enriched pathways with this method, both for the up and downregulated genes. I then…

clusterProfiler KEGG GSEA

updated 4.9 years ago • Emilia

I have, it seems to be working fine for all except for one dataset. This dataset is from the organism fly while the others are either mouse or human.When I  run deseq2 with 'LRT' for the fly dataset I get the following

deseq2 anova

updated 9.2 years ago • szenitha

Hi I have RNA seq data for six different treatments (A,B,C,D,E,F) of a model organism, with four-fold biological (NOT technical) replicates. FASTQC revealed no abnormalites in the RNAseq data and after

deseq2 rnaseq PCA hierarchical clustering outlier

updated 9.1 years ago • wd

analysis using enrichGO function through clusterProfiler. As I am going to analyze nonmodel organism seabream so I used AnnotationHub to build OrgDb. I retrieved the annotation database library(AnnotationHub) hub

software error enrichGO annotationHub clusterProfiler Job

updated 5.7 years ago • bnajafpour

baseName = "GEM.txt", srcUrls = mySrcUrls, baseMapType =myBaseType, pkgName = "GEM",pkgPath = myDir, organism = "Mus musculus", version = "1.0.0",author = list(authors = "joe", maintainer ="joe.joe at gmail.com"), fromWeb = TRUE) after the creation

Annotation Organism probe AnnBuilder Annotation Organism probe AnnBuilder

updated 18.4 years ago • claudio.is@libero.it

MoGene data collected for mouse using the following command: res = spia(de = DE, all = ALL, organism = "mmu", nB = 2000, plots = FALSE, beta = NULL) The procedure runs to completion and produces results and shows several pathways

Genetics Network Organism SPIA Genetics Network Organism SPIA

updated 15.4 years ago • Will Bush

but as far as we are able to understand the packages use the info available in the corresponding organism .db0 packages. However, it is not clear to us how now to continue with the mirna.db SQLite file we created. Any advice

miRNA Annotation db0 AnnotationDbi miRNA Annotation db0 AnnotationDbi

updated 16.2 years ago • Guido Hooiveld

with only one ORF sequence per gene. P.P.S. Alternative splicing isn't a consideration for this organism

deseq2 salmon

updated 7.6 years ago • andrewpountain

Analyst The EMMES Corporation, organized in 1977, is a privately owned Contract Research Organization (CRO) located in Rockville, Maryland. EMMES is dedicated to providing statistical and epidemiological expertise

Microarray Cancer Microarray Cancer

updated 17.2 years ago • Marcella Pickard

Hello, I have been conducting pathway analysis on my RNA-seq data using the Deseq2/GAGE workflow. I ran GAGE and it worked well generating a list of affected pathways. I used “KO” annotations from kegg.gsets (species=”ko”) as I am working on a non-model organism. I am now trying to extract data for essential member genes in my perturbed pathways with essGene() However, I keep getting...pathways.…

gage gage package

updated 9.2 years ago • Michael

F,prefix="primeview",fileName="primevie wHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANISM "="Homo sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="Pri meView Human Gene Expression Array","MANUFACTURERURL

updated 12.7 years ago • wang peter

baseName=myBase, srcUrls=mySrcUrls, baseMapType=myBaseType, pkgName="PRG_protein_pkg", pkgPath=myDir, organism="Oryza sativa", version="1.1.0", author=list(author="Ross", maintainer="ross.chapman at xxxxxxxx"), fromWeb=FALSE)} date() Can

Genetics Annotation AnnBuilder GOstats Genetics Annotation AnnBuilder GOstats

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

2) Make sure you have have the appropriate BSgenome.* package which has the genomic sequence for the organism you are working with. For instance, if you are working with human data with the hg19 release, you'd need the BSgenome.Hsapiens.UCSC.hg19

Cancer Organism BSgenome BSgenome Cancer Organism BSgenome BSgenome

updated 14.2 years ago • Steve Lianoglou

most people expect. And the pig org package is made (special) here along with all the other major organism packages that we support. It is not generated by the method you used because that method has to work for ALL organisms...not meant to be a way to get a newer package. It is meant to allow people who are using non-model organisms to get annotations. So it is expected that some things are …

Annotation GO Organism OrgDb Annotation GO Organism OrgDb

updated 13.8 years ago • Marc Carlson

Chromosome names of query and genome do not match > head(BSgenome,100) 1 function (organism, common_name, genome, provider, provider_version, 2 release_date, release_name, source_url, seqnames, circ_seqs...seqinfo) 11 if (missing(common_name)) 12 common_name <- species 13 metadata <- list(organism = organism, common_name = common_name, 14 genome = ge…

branchpointer

updated 3.9 years ago • alexandre.maucuer

function calls ... OK * checking R code for possible problems ... NOTE .onLoad: warning in BSgenome(organism = "Saccharomyces cerevisiae SK1", species = "Yeast", provider = "Hochwagen Lab", provider_version = "1.00", release_date = "Unsure...extdata_dir): partial argument match of 'seqs_dir' to 'seqs_dirpath' .onLoad: warning in BSgenome(organism = "Saccharomyces cerevisiae SK1", species …

Saccharomyces cerevisiae BSgenome Biostrings BSgenome Saccharomyces cerevisiae BSgenome

updated 11.6 years ago • Guest User

_Down")   CompKEGG\_limma <- compareCluster(geneCluster = list\_limma, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1) CompKEGG\_edge <- compareCluster(geneCluster = list\_edge, fun = "enrichKEGG",organism="hsa", pvalueCutoff...1) CompKEGG <- compareCluster(geneCluster = list, fun = "enrichKEGG",organism="hsa", pvalueCutoff=1) &nbsp

clusterprofiler

updated 8.5 years ago • joseph