Bioconductor Forum

am analyzing some ATH11 Affymetrix arrays, but I was not able to find the annotation files for this organisms and I cannot complete the analysis. Could you give me any help? thanks mirella</div

updated 20.7 years ago • lettieri@igb.cnr.it

<div class="preformatted">Hi Everyone, I have been using edgeR for quite sometime. Most of our RNAseq data comes from infectious organisms like Malaria and Tryps. Our libraries generally have 10 to 20% of the reads coming from rRNA genes (not sure if this is the typical value for other organisms/protocols). All these days, I have been ignoring them while doing the DE analysis using edgeR. …

RNASeq edgeR RNASeq edgeR

updated 12.7 years ago • gowtham

myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "Bioc_WG-6_anno", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", + author = list(authors = "FMB", maintainer ="FMB"), fromWeb = T) Attaching package: 'GO' The following...GO Error in parseKEGGGenome(url = kegggenomeUrl) : Faild to obtain KEGG organism code > -- Dr. Francesca Meteora Buffa,…

Annotation Organism AnnBuilder Annotation Organism AnnBuilder

updated 18.5 years ago • Francesca

user's manual ,it has been suggested to use a dispersion value of 0.1 in case of no replicates for organisms that are genetically similar to humans. so it is possible to be used for mouse data for example,what about other...organisms like yeast ?? As exact test is used to get DE genes across 2 samples and i need to get DE genes across my time course experiment

Yeast edgeR Yeast edgeR

updated 14.0 years ago • Asma rabe

Hi All, I have error during package generation for sugar beet (and other organism also). How can I fix it. Please help!    makeOrgPackageFromNCBI(version = "0.1", +      &nbsp...starting download for 5 data files getting data for gene2pubmed.gz extracting data for our organism from : gene2pubmed getting dat…

annotationforge makeorgpackagefromncbi

updated 8.4 years ago • gabciamm

<div class="preformatted">Hi, I found the KEGGgraph package in the development repository. It sounds great. But it is not working. There are no edges in the graphs! What is wrong? > library(KEGGgraph) > tmp <- tempfile() > retrieveKGML('04110', organism="hsa", destfile=tmp, method="wget", quiet=FALSE) --08:58:59-- ftp://ftp.genome.jp/pub/kegg/xml/organisms/h…

Organism hgu133a KEGGgraph Organism hgu133a KEGGgraph

updated 16.7 years ago • Markus Schmidberger

t be able to think of all the possible use cases (b) you're certainly much more familiar with the organism you are using than I am so you would know best the possible caveats (e.g. trans-splicing in fruitfly). There are methods...off-list) as it will help me finalize that vignette use case. If you agree, just tell me what organism you are working with and we can get started. If it's an organism n…

Annotation Organism PROcess GenomicRanges easyRNASeq Annotation Organism PROcess

updated 13.2 years ago • delhomme@embl.de

Hello, I have more of a general question. I am annotating CD4+ / CD8+ T cell subtypes in a non-model organism. What metrics would you use to label a cluster as Cd4+ with some level of confidence? Anything other than non-zero median

SingleCellExperiment

updated 17 months ago • georgii.vdovin

to use the git.bioconductor.org repository, a 'ssh' key is needed. Actually the package is hosted on organization account and I can not set a key for it. I was wondering if is there anyway to branch my account and to use my authenticity

SSH git

updated 3.6 years ago • Loubna

the BSGenome list.  I´m intersted due to we are trying to use the CRISPRseek package for this organism. Here is the link: https://www.ncbi.nlm.nih.gov/genome/?term=Leishmania+panamensis Best regards

bsgenome

updated 8.3 years ago • sneider.gutierrez01

<div class="preformatted"> Dear all, In the past, SPIA package included KEGG pathway topology information for SPIA analysis for human and mouse organisms. Since the access to the KEGG ftp currently requires a license, we have discontinued the practice of including up to date KEGG pathway data in the SPIA package. However, the users will still be able to use up-to-date pathway data for the o…

Organism SPIA Organism SPIA

updated 12.8 years ago • Tarca, Adi

<div class="preformatted">The example is a simple two group design where one group is treatment and the other is control. There should be no need to re-organize your files, but it important to provide a sheet / targets file giving the location of the files as well as relevant phenodata...group design where one group is treatment and the other is control. There should be no need to re-orga…

Normalization minfi Normalization minfi

updated 12.7 years ago • Kasper Daniel Hansen

commercial $750. Proceeds from this course fund the Bioconductor Foundation, a 501(c)3 nonprofit organization that provides scholarships to the Bioconductor conference. [[alternative HTML version deleted]] </div

updated 14.2 years ago • Vincent J. Carey, Jr.

there is a package for primers design. The design should consider codon usage table from different organisms and design the best oligos for PCR. Thanks a lot in adavnce for help. Fab</div

updated 22.2 years ago • Fabien Crozet

y-Axis Label", name="Author", lab="Address", abstract="Abstract", url="URL", annotation="Annotation", organism="Organism"), coldata=coldata, rowdata=rowdata) Any suggestion would be great. thanks kavit -- output of sessionInfo(): locale

GO GO

updated 14.0 years ago • Guest User

Hi All, Sorry if this is too basic, I have read through a bunch of forum posts already but I don't find an answer to this. I want to run GOstat to calculate GO term enrichment in Differentially expressed genes (DEGs) vs. a background gene Universe which = the reference transcriptome. \[I work with a non-model organism\]. I have GO annotations from Blast2GO for my DEGs, exported in GOstat forma…

GOstat format input files

updated 9.7 years ago • bannistersc

Now I am wondering if it is possible for me to create a separate, private hub for my organization to host data that cannot be shared externally? Perhaps there is a code repository that documents how the official

ExperimentHub

updated 3.4 years ago • sandmann.t

<div class="preformatted"> Dear All and Nico, Have anyone be able to do the counting from C.elegans? Here is what I tried but result in no luck: 1) bam was generate from tophat1.4.1, with ucsc ce6 as reference. For easyRNASeq counting, the *.rda was used as reference (see the code below) obj <- fetchAnnotation(new('RNAseq', organismName="Celegans" …

Alignment Annotation Organism Alignment Annotation Organism

updated 13.6 years ago • Yonggan Wu

of homo sapiens I get the below error. It works fine for drosophila. > retrain(KEGG.package=TRUE, organism="hsa") Retrieving KEGG information via KEGG.db package ... done Retrieving information from InterPro database for...organism ' hsa ' via Ensembl ... Checking attributes ... ok Checking filters ... ok Error: cannot allocate vector of size 248.4 Mb > sessionInfo

Pathways GO Organism Homo sapiens hgu133plus2 gene2pathway Pathways GO Organism

updated 16.2 years ago • Kishor Tappita

that I am using a custom OrgDb which doesn't have the `go_bp` table. A custom OrgDb for a non-model organism that I made using `AnnotationForge::makeOrgPackageFromNCBI()` has these tables: `tbls: accessions, alias, entrez_genes...is that we are encouraged to use `select()` and `columns()` and `keytypes()`, but using a non-model organism and the error message from `pca2go` about a particular m…

annotation go pcaExplorer AnnotationForge

updated 6.8 years ago • psutton

novo transcriptome in Trinity. I then aligned the reads back to the assembly using RSEM. This is an organism that does not have an annotated genome. Is it possible to use DESeq and upload my data via tximport? I have a text file

RSEM tximport deseq2

updated 5.5 years ago • pthom010

KO IDs for my genes. Does gage support bacteria genomes? than, I saw that you need to specify the organism name, but I'm not interested in a specific bacterial species. Is it possible to use it with KO ids from different species

gage pathways kegg

updated 11.0 years ago • francesca.defilippis

<div class="preformatted">I am having a problem with the chromLoc object while trying to use the cset2band method in the reb package. I am trying to do a genome wide cytogenic analysis. Here is my full code. library(affy) library(hgu133plus2.db) library(hgu133plus2barcodevecs) library(hgu133plus2cdf) library(idiogram) library(reb) expr <- justRMA() matrix <- assayData(expr…

Organism hgu133plus2 reb Organism hgu133plus2 reb

updated 15.5 years ago • Sathe, Tejas

GOMF")) # Error in chipenrich(head(peaks), out_name = NULL, genome = "mm10") : # Invalid organism / geneset(s) combination requested: mmu TRUE # In addition: Warning message: # In if (file.exists(genesets)) { : # the condition...chipenrich() ``function. For `` "mmu" `` and these gene sets: <pre> any(supported_genesets()$organism == "mmu" & c("GOBP", "GO…

chipenrich

updated 8.8 years ago • jamie.gearing

i am doing Gene ontology for my RNAseq data , Salmonella is not a model organisms so that i used annotationforge package to create org.db annotation package for it. then i tried to retieve the...i am doing Gene ontology for my RNAseq data , Salmonella is not a model organisms so that i used annotationforge package to create org.db annotation package for it. then i tried to retieve the package

annotation

updated 5.9 years ago • shamed

<div class="preformatted">Dear list, In terms of dbSNP database in NCBI, I can get the chr_rpts files for the most recent 37.3 assembly from the following FTP site, ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/chr_rpts/ My question is how/where I can get these chr_rpts files based on the 36.3 assembly Thanks, Shirley...files for the most recent 37.3 assembly from the following FTP si…

updated 14.1 years ago • shirley zhang

I have chromosomal location or genome coordinates for list of miRNAs. Please advice me how can I make a figure to better visualize this data ? I am interested in figures like this ( Figure 3) https://www.researchgate.net/figure/Genomic-organization-of-14q32-microRNA-miRNA-clusters-neighboring-the-DLK1-DIO3_fig3_51466062 https://erj.ersjournals.com/content...I am interested in figures like this…

cancer

updated 6.5 years ago • angajalaanusha

Dear BioC team, I noticed that all of the [BioC docker images](http://bioconductor.org/help/docker/) are based on the [rocker/rstudio](https://hub.docker.com/r/rocker/rstudio/) image, which contains [Rstudio-server](https://www.rstudio.com/products/rstudio/). I am a big fan of Rstudio's products myself, but Rstudio-server [uses the AGPL licsense](https://www.rstudio.com/faq-items/work-commercial…

docker

updated 9.5 years ago • Thomas Sandmann

Hello, I started an enrichment analysis but I'am stuck with the enrichment part, my organism is not in the list of supported organisms so I made my custom annotation. When I use the enricher function I just get

clusterprofiler

updated 9.6 years ago • naholi.alejandri

<div class="preformatted">Bioconductor basics course in Boston, 24-25 October -- space is limited Tentative agenda --- Oct 24 (Monday) 9am-12pm Vince Carey (VJC, bioconductor core): introduction, software setup, basic programming and structures, annotation 12pm-1pm (lunch on your own) 1pm-4pm Aedin Culhane (Dana Farber Cancer Institute): on clustering/ordination, reproducibility 4pm…

Genetics Cancer Genetics Cancer

updated 14.2 years ago • Vincent J. Carey, Jr.

There are two biological replicates per cell type. Furthermore, the cell types belong to one of two organ classes. In order to generalize this for convenience, I label the organ classes o1 and o2, and the cell types within each...class c1, c2, and c3. Additionally, the cell type replicates are r1 and r2. So I have for organ class 1, the samples   o1-c1-r1 and o1-c1-r2   o1-c…

deseq2

updated 8.3 years ago • bge

Dear Sir/Madame, I am looking for a software to analyze array (comparative genomic hybridization) CGH data that does not require genome mapping because I am working on ants, which genome sequence and mapping are not available. Thank you in advance. I appreciate your reply. Best regards, Mingkwan

CGH CGH

updated 17.0 years ago • Mingkwan Nipitwattanaphon

Dear Tae-Hoon, Thanks for the bug report. KEGG changed their FTP site structure on March 31. I have updated AnnBuilder. The lastest version is 1.13.23 which is available at svn repository now. You can get it via biocLite tomorrow. thanks nianhua

AnnBuilder AnnBuilder

updated 18.7 years ago • Nianhua Li

Note: I have posted this on GitHub, as this seems more appropriate but I do not know how to remove a post. I annotated using ChIPseeker mouse chip-seq data (aligned to GRCm38). I am interested in seeing the distribution of all the **reads**, not only of the peaks. For this purpose, I have downsampled the alignment bam files to 1M reads, and converted the file to bed format (hope this is kosher…

ChIPseeker

updated 5.0 years ago • Sam

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updated 18.2 years ago • Urska Cvek

Hello, apologies, I am confused by the following. It seems that people often use Deseq2 to identify differential amplitude of gene expression, but dexseq to identify alternative splicing. However, Deseq2 can kindof give alternative splicing information if analysis is done at transcript level rather than gene level. The species I work with (ants and bees) have almost no preexisting …

deseq2 splicing

updated 7.6 years ago • yannickwurm

Hi all, I am using goseq to correct for RNA-seq length bias. Since my dog genome (canFam3) is not supported in goseq database, I tried to make TXDb object and GOmap by myself. However, I am not sure if I am doing it correctly. __If it's correct, it could potentially be a tutorial and benefit other users since the goseq documentation isn't very self-explanatory. __ I ha…

deseq2 goseq biomart r rnaseq

updated 9.6 years ago • CandiceChuDVM

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070329/ 15d71471/attachment.pl

updated 18.7 years ago • Tae-Hoon Chung

Dear All, The affy platform annotation packages available in bioconductor do not have "rice" included. Is there a way i can still use this in R? Any suggestions would be highly appreciated. Thank you Ekta Jain Research Analyst Biotechnology and Bio-resources Division The Energy and Resources Institute, India Habitat Centre Lodhi Road, New Delhi - 110033 #099…

Annotation affy Annotation affy

updated 12.6 years ago • Ekta Jain

I am working with a non model organism and I performed a gene set enrichment test using topGO and GOstats. The analysis in both cases worked properly, but

topgo gostats go

updated 11.2 years ago • artur

keggID <- "05213" > > tmpXML <- "testKGML2.xml" > > retrieveKGML(pathwayid=keggID, organism='mmu', destfile=tmpXML, > method="wget") > --2010-09-21 13:56:37-- > > ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- metabolic/organisms...gt; > --2010-09-21 13:56:39-- > > ftp://ftp.genome.jp/pub/kegg/xml/kgml/non- met…

Pathways KEGGgraph Pathways KEGGgraph

updated 15.2 years ago • Jitao David Zhang

div class="preformatted">Hi , I am trying to build an annotation organism package by using Annotation Forge package. I followed this document<http: 2.12="" anno="" bioc="" doc="" inst="" newschema.pdf...are they to be modified to be able to access the data in the sqlite db that I am creating for the organism I am working on. ========================== > cols(org.At.tair.db) [1] …

Annotation Organism AnnotationDbi Annotation Organism AnnotationDbi

updated 12.3 years ago • Rameswara Sashi Kiran Challa

basefile,"Basefile.txt",sep="\t",row.names=F) library(AnnBuilder) mySrcUrls=getSrcUrl("all",organism="Homo sapiens") ABPkgBuilder(baseName = read.table("Basefile.txt",header=F,sep="\t"), srcUrls = mySrcUrls, baseMapType ="ll...pkgName = "hgu133plus2", pkgPath = getwd(), organism = "Homo sapiens", version = "1.1.0",author = list(authors = "K"),fromWeb=TRUE) Error in validObject(.Object) : inv…

Organism AnnBuilder Organism AnnBuilder

updated 17.3 years ago • Kamila Naxerova

that are kind of related to each other. 1) Solanum lycopersicum is not among the org.db model organism supported by clusterprofiler. I tried to import the AnnotationHub Solanum as following but it doesn't seem to work...UNIGENE" I was trying to play around and/or find the way to use clusterProfiler from non model organism, and see if i can start from this kind of table format uniprotID …

clusterProfiler AnnotationHub GO uniprot

updated 4.8 years ago • Alberto

Females and males display striking patterns of sexual dimorphism in many animals and other organisms. Differences are documented in morphology, physiology and behaviour. In recent years, advances in genomics technologies...will focus on the molecular basis and evolution of sexual dimorphism across animals and other organisms, including the origins, evolution and biology of sex chromosomes. It wil…

events biology sexual dimorphism conference News

updated 5.9 years ago • EMBL Events

genomics, it so frustrating for me to use R for data analysis work. That too working with non-model organisms no one had heard of before. After de novo assembly step I used salmon for quantification and generated the quant.sf...I combine all the matrices into a single matrix which I'll be fed into DESeq2/EdgeR packages. The organism I'm working for doesn't have any information in the public doma…

tximport deseq2 edgeR

updated 5.5 years ago • sunnykevin97

hgu95av2") >newChrom Instance of a chromLocation class with the following fields: Organism: Homo sapiens Data source: hgu95av2 Number of chromosomes for this organism: 25 Chromosomes of this organism and

Organism geneplotter Organism geneplotter

updated 20.7 years ago • Giulio Di Giovanni

package. But instruction in "how to use AnnBuilder" stated that parameter of function ABPkgBuilder:organism now only can be "human", 'mouse", or "rat". This means that I can not use arabidopsis instead, right? Thanks a lot. Josh</div

Annotation Annotation

updated 21.3 years ago • szhan@uoguelph.ca

div class="preformatted">Hi All The platform for GSE4137 is "Custom cDNA 41,424 clones", and organism is human. I tried the code which you mentioned,but gives me error:- get("AA502230",revmap(org.Hs.egACCNUM)) Error in .checkKeys

Organism Organism

updated 13.9 years ago • Reema Singh

to shed some light on the following error. It's generated when I attempt to access the supported organism list in goseq.  __> supportedOrganisms()__ __Error in getNodeSet(doc, "//table\[@class='descTbl'\]")\[\[1L\]\] :    subscript

goseq

updated 8.8 years ago • jesykamelendez

not including GoogleGenomics in Bioc 3.8, and archiving the github repo under the Bioconductor organization. I tried to find self-service steps, but could not find any. Thank you. Sid

bioconductor

updated 7.4 years ago • sidb

perform searches on the zebrafish genome, but am unable to find a TxDb file for this widely studied organism. Is there a mechanism to request that a TxDb file be prepared for Drerio? Thank you, Mike Brodsky </div

Organism zebrafish CRISPRseek Organism zebrafish CRISPRseek

updated 11.8 years ago • Brodsky, Michael

at least like to try (I do enjoy using R!) It is long-read RNAseq from cDNA, control vs disease, organs brain, lung(model1), lung(model2-reflects different phenotype of disease). I have removed adapters, then mapped reads...For example isoformswitchanalzer. This is the first time long read sequencing is done on these organs in this disease so I don't have a particular question, I have been told …

DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq

updated 20 months ago • 09191919

sort(foldchanges, decreasing = TRUE) set.seed(123456) gseaKEGG <- gseKEGG(geneList = foldchanges, organism = "mmu", nPerm = 1000, minGSSize = 20, pvalueCutoff = 0.05, verbose = FALSE) sessionInfo( ) ``` This is the message I get when running...seems similar. ```r data(geneList, package="DOSE") kk2 <- …

KEGG clusterProfiler

updated 2.8 years ago • redafazazi

The Bioinformatics & genomics unit at Molecular Biotechnology Center (Torino, Italy) organizes an introductory course on RNAseq on 17-19 March 2015 This hands on course is suitable for biologists who are new...RNAseq.course.html Registration site: http://www6.unito.it/.RNAseqCourse/   [The Organizer]( http:=) [Raffaele A Calogero]( http:=) <pre> <a href=" http:="&…

rna-seq course News

updated 10.8 years ago • rcaloger

Hello, I have been trying to use makeOrgPackageFromNCBI for what I believe is a well-annotated organism (Acropora millepora, taxon ID 45264). After being unsuccessful, I tried to run the example from Mark Carlson from this...approach using inputs that I found from a published article that successfully did it with another organism: > makeOrgPackageFromNCBI(version = "0.1", + …

annotationforge makeOrgPackageFromNCBI

updated 5.8 years ago • lesneski

WThypo) [1] "11535" "20525" "11839" "15277" "11910" "18639" >res=spia(de=WThypo,all=HWThypo1,organism="mmu",nB=2000,plots=F,beta=N ULL,combine="fisher",verbose=F) Error in spia(de = WThypo, all = WThypo1, organism = "mmu", nB = 2000, : de must

Organism SPIA Organism SPIA

updated 14.3 years ago • Jing Huang

HI I some how, figure out the manual to reproduce the same plots for my data. I'm working with non-model organism it doesn't have a annotation information or package for GO/KEGG analysis. I had ~4 experimental setup, after edgeR analysis...some how, figure out the manual to reproduce the same plots for my data. I'm working with non-model organism it doesn't have a annotation information or …

clusterprofiler

updated 5.4 years ago • sunnykevin97

r > human_projects <- available_projects(recount3_url = "http://duffel.rail.bio/recount3", organism = "human") Error in `collect()`: ! Failed to collect lazy table. Caused by error in `db_collect()`: ! Arguments in `...` must be used. x Problematic

recount3 recount

updated 22 months ago • Max Bone

Hello, I'm looking at the featureCount flag -t and the gtf file for my organism of study, and the gtf file has the following feature options: gene, exon, transcript, and CDS. The manual indicates that

Rsubread featureCounts RNASeq

updated 2.1 years ago • HS