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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 17.3 years ago • Hongping Wu

rows> (or 0-length row.names) I tried it with other species, and found out that it finds many organisms (e.g. 'mmu', 'dre'), and doesn't find many other organisms (e.g. 'malb', 'els'). What can I do about it? And does it mean that the package

software error go

updated 5.9 years ago • poisk.kirpitcha

nbsp;                 organism = "mouse",#organism = "human"<br/>                    o…

software error clusterprofiler GO genesetenrichment

updated 9.7 years ago • José Luis Lavín

four number of Two-color array chips (.gpr files/ genepix) with different time points, infecting organism and with dye swaps and some having biological replicate. it's getting complicated for me to make design/contrast...with Virus; CDLW = Carborundum-dusted leavestreated with Water\]   <pre> <code>Sample_title Organism Geo protocol_1 Label_1 protocol…

microarray limma design and contrast matrix

updated 7.7 years ago • 1234anjalianjali1234

__Joint interdisciplinary postdoctoral positions in the research groups of:__ * Detlev Arendt, European Molecular Biology Laboratory (EMBL) * Wolfgang Huber, European Molecular Biology Laboratory (EMBL) * Henrik Kaessmann, Center for Molecular Biology (ZMBH), Heidelberg University Cell types are the fundamental units of multicellular life. They make up distinct tissues and organs in verte…

evolution single-cell development differentiation cool Job

updated 9.5 years ago • Wolfgang Huber

with the error: ``` Segmentation fault (core dumped) ``` The largest chromosome in this organism is over 2Gbp. I suspected that it may be because of these large chromosomes. To test this, I systematically removed

Rsubread

updated 14 months ago • vkkodali

ont ="ALL", keyType = "ENSEMBL", pvalueCutoff = config_pvalueCutoff, verbose = TRUE, OrgDb = organism) readable_gene_names <- setReadable(gse, 'org.Hs.eg.db', 'ENSEMBL') heatplot(readable_gene_names, foldChange=gene_list

heatplot enrichplot

updated 3.0 years ago • Melanie

Hello! I work with a nonmodel organism that does have a valid KEGG species code listed here: https://www.genome.jp/kegg/pathway.html This is the command

KEGGREST KEGG gage pathview

updated 3.4 years ago • nute11a

Used 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 me in finding

goProfiles goProfiles

updated 12.4 years ago • Guest User

KEGG pathways? >thanks >Bhaskar Hi Bhaskar, The latest KEGG data matrices for SPIA for most organisms in KEGG are at: http://bioinformaticsprb.med.wayne.edu/SPIA/SPIA_KEGG_dec082010/ Note that not all the pathways

Pathways SPIA Pathways SPIA

updated 15.1 years ago • Tarca, Adi

gvrocha at gmail.com", biocViews = "AnnotationData", genomebuild = "hg19", organism = "Homo sapiens", species = "Homo sapien", url = "http://about.me/gvrocha") makePdInfoPackage(seed, destDir=".") -- Guilherme V. Rocha

BiocViews Annotation Organism biocViews pdInfoBuilder BiocViews BiocViews Annotation

updated 11.3 years ago • Guilherme Rocha

KEGG species (about 2300 to date and more forthcoming). This is important for studies on none model organisms or rare species. In the meantime, Pathview also supported KEGG Orthology (with species="ko"). This makes pathway analysis

Visualization gage pathview Visualization gage pathview

updated 12.2 years ago • Luo Weijun

mymail",          genomebuild="hg38",          organism="Homo Sapiens",          species="Homo Sapiens",          version = "0.0.1")</pre> <pre> makepdInfopackage

limma pdinfobuilder affy cdf

updated 8.8 years ago • yusuf.khan

nbsp;                 organism="Candida glabrata",format="gff3",                 &nbsp

bsgenome genomicfeatures

updated 7.4 years ago • michael.weber.1

Exploring Genomic Data Using R and BioConductor * Writing R Extensions * R Graphics For the organization committee Achim Zeileis ------------------------------------ Achim Zeileis Institut für Statistik Technische Universität Wien http://www.ci.tuwien.ac.at

updated 22.9 years ago • Achim Zeileis

div class="preformatted">Dear All, I am currently using an Agilent 4x44K model organism mosquito array for a one color time-course course experiment. I am analyzing using the LIMMA package and have performed

Normalization Organism limma Normalization Organism limma

updated 13.5 years ago • Mitchell, Sara N

baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "myPkg", pkgPath = myDir,organism = "Homo sapiens", version = "1.1.0", fromWeb = TRUE)} Attaching package: 'GO' The following object(s) are masked from package:AnnBuilder

Annotation Annotation

updated 19.5 years ago • Dario Greco

enrichment analysis I want 1. what kind of input file it can take eg(csv) is okay? 2. which organism it supports I am trying to use for mouse ? 3. I tried for my sample gene lists using Enterz id but every time no map found

bioconductor

updated 8.8 years ago • azhar

to make it faster would be helpful. A small part of code is "ensembl = useMart("ensembl", dataset = organism) godata<-getBM(attributes = c(list_type,"go_id","name_1006"), filters = list_type, values = genelist[,1], mart = ensembl) godata

Annotation GO PROcess biomaRt Annotation GO PROcess biomaRt

updated 11.4 years ago • Konika Chawla

div class="preformatted">hi, while i was using the gene-centric organism-level package for yeast org.Sc.sgd.db i encountered the following error: library(org.Sc.sgd.db) select(org.Sc.sgd.db

updated 12.6 years ago • Robert Castelo

we used padj<0.05) and kept on insisting that the number of samples is too low ( 7 cadaveric organ donors samples cultured in 2 conditions (paired) for mRNA and ChIP-Seq) for differential analysis and asked for a measure

deseq2

updated 6.7 years ago • gthm

1] where you can discuss or ask questions. Announcements will also be made by the [@Bioconductor organization on Twitter][2] using the #bioc2020 hashtag. Some key dates: | Mark the date! | | |------------|-----------| | Jan 9 | Registration Opens | |Jan 15 | Call for

conference News

updated 6.1 years ago • Levi Waldron

but found them very helpful so I'm trying to use. Now I need to make a BSgenome pckg for my own organism. Therefore I have made a folder named seqs_srcdir which contains 17,000 files (one gene_sequence per file), but when

Organism BSgenome BSgenome Organism BSgenome BSgenome

updated 12.0 years ago • Guest User

as a node? ```r > path_id <- "dre03320" > > retrieveKGML(pathwayid = path_id, organism = "dre", destfile = paste("tmp_dir/", path_id, ".kgml")) trying URL 'https://rest.kegg.jp/get/dre03320/kgml' downloaded 25 KB > &gt...kgml")) > path KEGG Pathway [ Title ]: PPAR signaling pathway [ Name ]: path:dre03320 [ Organism ]: dre [ Nu…

igraph KEGGgraph RCy3 GraphNEL

updated 15 months ago • Arindam

dataSource=my gff file", format="gff3", organism="unknown organism")</pre> but including the annotation lead to another problem. I am very new to genomicfeatures package

chipqc R

updated 8.5 years ago • tuteja.reetu

Aedes-aegypti-Liverpool_REPEATFEATURES_AaegL3.gff3", format="auto", dataSource = "EnsembleMetazoa", organism = "Aedes aegypti") Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make...TxDb object: #Db type: TxDb #Supporting package: GenomicFeatures #Data source: EnsembleMetazoa #Organism: Aedes aegypti #Taxonomy ID: 7159 …

maketxdbfromgff

updated 10.1 years ago • rebecca.halbach

Hi all, I would like to ask your expert opinions related to microarray experiments with Drosophilas. I have been asked to conduct a microarray experiment. According to the study design (pilot study) I need 2-4 groups : 1st->3rd treatments + 4th control. For each group 8-10animals would be ideal for the statistical power we want to achieve. (4 array groups - 8 arrays per group) If the experi…

Microarray BRAIN Microarray BRAIN

updated 15.2 years ago • Paparountas Triantafyllos

I have been following the workflow available at \[Importing transcript abundance datasets with tximport\]() and it is required to use a TxDb object. I am working with Rice and there isn't a TxDb object for rice. But rice has a BSgenome object. Is there any way I can use the BSgenome object? I just want to use my Salmon output to be used in DESeq2.

tximport deseq2 annotationdbi

updated 8.3 years ago • prab4th

I wanted to use EnsDb.Hsapiens.v86 and org.Hs.eg.db combined, as both databases do not exactly display the same type of information (for example, only EnsDb.Hsapiens.v86 provides with biological function, or list of exons). However, as you can see on below code, I was quite disappointed to notice that a great number of SYMBOL genes of org.Hs.eg.db weren't in EnsDb.Hsapiens.v86, and respective…

AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db

updated 4.9 years ago • bastien_chassagnol

thinks the database will be exactly 12GB - surely that depends on how much info there is for the organism in question? I checked the help files (e.g. ?\`OrgDb-class\`), and they don't seem to say what's in the db.  Cheers! Luke &nbsp...br/> getting data for gene2pubmed.gz<br/> rebuilding the cache<br/> extracting data for our organism from : gene2pubmed<br/>…

annotationforge

updated 7.4 years ago • lukeholman

a beginner user of KEGGSOAP and for my application i need the function list.pathways(org) for human organism. I have noticed that there are some problems with this function and i wanted to know if it provides all of the pathways

Pathways Organism KEGGSOAP Pathways Organism KEGGSOAP

updated 13.4 years ago • Jenny Kar

I am trying to create a TxDb for a non-model organism. The genome is annotated on NCBI and the associated GO files, etc are on there. So, I am trying to use the makeTxDbFromGAF...I am trying to create a TxDb for a non-model organism. The genome is annotated on NCBI and the associated GO files, etc are on there. So, I am trying to use the makeTxDbFromGAF() function. I continue to get the same erro…

AnnotationHub AnnotationDbi AnnotationForge

updated 16 months ago • Anna

REFERENCE/Homo_sapiens.GRCh38.98.gtf.gz' makeLinkedTxome <- function(indexDir,source,organism,release,genome,fasta,gtf,write=TRUE,jsonFile) {indexJson <- file.path(indexDir,"info.json") indexList <- fromJSON...source <- src } } } makeLinkedTxome(indexDir=indexDir,source="Ensembl",organism="Homo sapiens", release="98", genome…

tximeta

updated 5.9 years ago • Fei Liu

<div class="preformatted">Dear Gowthaman, There's no rigorous answer to this question, because it depends on the variability of your population, how large the fold changes are that you want to detect, how many genes you need to find, what FDR you can tolerate, etc etc, and it's impossible to know all these things in advance. However, we can learn from experience. At our institute, we reg…

RNASeq Organism edgeR RNASeq Organism edgeR

updated 13.6 years ago • Gordon Smyth

gt;>Windows Live Hotmail with drag and drop, you can easily move and organize >>your mail in one simple step. Get it today! >>www.newhotmail.ca?icid=WLHMENCA153 >> > > _________________________________________________________________...Windows Live Hotmail with drag and drop, you can easily move and organize www.newhotmail.ca?icid=W…

Microarray Normalization GeneTraffic lumi Microarray Normalization GeneTraffic lumi

updated 18.6 years ago • Longsi Ran

genes found in universe" Is there a reference for implementing a species with a corresponding organism package in goana? I have been following this vignette for reference: https://www.bioconductor.org/packages/devel

org.Dr.eg.db zebrafish limma

updated 6 months ago • Eric

Dear Bioconductors, 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 …

bioconductoroversight community CAB

updated 3.9 years ago • shepherl

Hi all, Kindly guide me. I am a beginner, exploring scRNAseq analysis. I want to combine different scRNAseq studies on various tissue to find how gene profile changes in all of them. For example - Altered Gene Expression Profiles in the Brain, Kidney, and Lung of One-Month-Old Cloned Pigs So here my scRNA seq data say hypothetically be- gse ... brain dropseq year 2015 …

scRNAseq

updated 4.3 years ago • SG

OrgDb = "org.At.tair.db", keyType = "TAIR",ont = "BP") > ego # # over-representation test # #...@organism Arabidopsis thaliana #...@ontology BP #...@keytype TAIR #...@gene chr [1:754] "AT1G55230" "AT1G55240" "AT1G55380" "AT1G55390" "AT1G55420

enrichGO

updated 4.6 years ago • dailing57

I am interested in quantifying the microbial content of an RNAseq experiment in a way that allows for statistically comparing abundances of species between samples. There are a few tools that have been built for this that I am using, but I was curious to hear if anyone has thoughts on using pseudo-alignment (Salmon) and DESeq2 for this. The workflow I've tried is as follows: 1) Map reads to th…

salmon deseq2

updated 7.0 years ago • kballa

model design to compare the differences between 2 treatments and 2 factors. I need help in trying to organize the model design matrix in EdgeR. How can I write the code for them to be recognized? I also need to make sure my replicates

edger design model interaction model rnaseq

updated 7.0 years ago • cody0071

baseMapType="gb", pkgName="OperonHumanV3", pkgPath=pkgPath, organism="Homo sapiens", version=version, author=list( authors="YourName", maintainer="YourName <youremail at="" email.com="">" ) ) } operon

Annotation GO Annotation GO

updated 19.1 years ago • Nianhua Li

That is, probes where designed based on desired genes that we wanted to capture from the micro-organisms in the samples. The reads were assembled and the contigs were functionally annotated by KEGG, thus I have a count

deseq2 metagenomics

updated 9.1 years ago • Earendil

<div class="preformatted">Dear Bioconductor users, I am trying to build a custom .cdf file for a custom Affymetrix genechip for an atypical model. The genechip has many features: orfs, SNPs, introns/exons (for one chromosome), antisense etcâ¦ I believe the design is fairly unique (PMID= 20974003; http://www.biomedcentral.com/1471-2164/11/603/table/T1) but as far as I understand the defaul…

Annotation cdf probe makecdfenv Annotation cdf probe makecdfenv

updated 13.9 years ago • Olivier Lucas

for zea mays (maize) as provided by MaizeGDB and stored in Biostrings objects. Version: 1.0.00 organism: Zea mays ssp. species: plant provider: MaizeGDB provider_version: zmv2 release_date: Dec. 2014 release_name: Maize

bsgenome

updated 11.0 years ago • qiwang1993

the scripts, without guarantee that those changes would remain compatible with future changes in the organization of the bioconductor repository. Hope you will find this useful. Best regards, Thierry -- Dr. Thierry Sengstag - Physicist

Cancer Cancer

updated 19.2 years ago • Thierry Sengstag

comparisons (Group1_1412.bam). Here's how I used the easyRNASeq function: DGElist = easyRNASeq(organism="Hsapiens", annotationMethod="biomaRt", gapped=TRUE, count="genes", summarization="geneModels", filesDirectory=getwd

biomaRt easyRNASeq biomaRt easyRNASeq

updated 12.9 years ago • René

RNA (guanine-N7)-methylation 1 1 9 GO:0043252 sodium-independent organic anion transpo... 1 1 10 GO:0045666 positive regulation of neuron differenti... 1 1 11 GO:0045721 negative regulation of

topGo gene enrichment ontology analysis

updated 6.4 years ago • s.bourne

needs? http://baderlab.org/Software/EnrichmentMap Last, I'm working with bacterial data, non-model organism. Thanks for your help. Best, Bernardo -- *Bernardo Bello Ortí* PhD student CReSA-IRTA Campus de Bellaterra-Universitat

GO Network GUI Organism GO Network GUI Organism

updated 12.1 years ago • biotech

N columns for N samples > rownames(logR) = letters[1:4] # probes are named a,b,c,d here > organism = "hsa" # for human or "mmu" for mouse finally you use these to initialize a new MEDMEset: Mset = new('MEDMEset', chr=chr, pos=pos...logR=logR, organism=organism) Now, in you case you have to load all these data from your files. I could not find chromosomal assignment and...comm…

Normalization Organism probe MEDME cycle ASSIGN Normalization Organism probe MEDME cycle

updated 17.1 years ago • Prashantha Hebbar Kiradi [MU-MLSC]

and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birth place of many fundamental discoveries in biology and medicine...would be advantageous, but are not required. In addition, the role requires good communication and organization skills, the ability to work well in a team, as well as an adv…

Switzerland JobPosting Basel Proteomics

updated 5.1 years ago • Robert Ivanek

625 - $775); this is necessary to receive the lower conference room rate from the hotel. The PSB organizers have been very helpful and generous in enabling us to add this workshop to the PSB, and we think there will be much...the PSB, go to http://psb.stanford.edu <http: psb.stanford.edu=""></http:> . Yours Sincerely, The Organizers of the PSB Extended Workshop on Alternative Splici…

Microarray Annotation GO Microarray Annotation GO

updated 22.1 years ago • Wang, Hui

getting data for gene2pubmed.gz rebuilding the cache extracting data for our organism from : gene2pubmed getting data for gene2accession.gz rebuilding the cache Error in scan(file = file, what = what, sep

AnnotationForge

updated 3.3 years ago • teddy1

Deadline for Community Advisory Board Nominations is this Friday February 25. Dear Bioconductors, 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 Bioconduct…

bioconductoroversight community CAB

updated 3.8 years ago • shepherl

ramakar = recount3::create_rse_manual( project = "SRP073813", project_home = "data_sources/sra", organism = "human", annotation = "gencode_v29", type = "gene" ) ramakar.exp <- assay(ramakar, "raw_counts") all(apply(apply(ramakar.exp

recount

updated 2.4 years ago • urwah

basic analysis data(geneList, package="DOSE") kegg <- gseKEGG(geneList = geneList, organism = 'hsa') # plotting cnetplot(kegg, categorySize="pvalue", foldChange=geneList)</pre> I want to change two things in this cnetplot

clusterprofiler pathway analysis pathways

updated 7.6 years ago • Mr.RB

srcUrl = ugUrl, parser = file.path(pkgpath, >"scripts", "gbUGParser"), baseFile = "geneNMap", >organism = "Homo sapiens", built = "N/A", fromWeb = FALSE) >parseData(ug) The geneNMap file has the entries: 32468_f_at D90278;M16652

updated 19.0 years ago • Benjamin Otto

I have single ended RNAseq reads from an allopolyploid organism. This means that I will have groups of 2,3, or even 4 genes with high sequence homology among them. I am sure some reads

deseq deseq2 edger tophat bowtie

updated 10.5 years ago • ysdel

div class="preformatted">Hi Everyone. Is there an organization that can be hired to train our scientists in Bioconductor? We would like to sponsor a training in house. Is there

updated 21.2 years ago • Eric.Grund@serono.com

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 6.2 years ago • daniel.magnus.bader