Bioconductor Forum

I have this simple question: **how a gene modifies the transcriptional response of an organism to a treatment?** I collected RNAseq data for a wildtype (WT) and a mutant (Mut) under treatment (t) or no-treatment (u). Factor...to my original question: “how my favorite gene “myFGen” modifies the transcriptional response of an organism to a treatment.” I will say that this is my “baseline” …

deseq2 interactions

updated 6.7 years ago • colaneri

gt; 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 • Gordon Smyth

Hello, I was trying to check kegg enrichment analysis for my Bulk RNAseq DGE results, and I am getting this error --> No gene can be mapped.... --> Expected input gene ID: --> return NULL... could you kindly tell what might be gone wrong? input: KeggSegGen <- shrink.tab %>% drop_na(Entrez,FDR) %>% dplyr:: filter(FDR < 0.05)%…

cluster clusterProfiler KEGG

updated 2.7 years ago • ruba-mahmoud

forward to see you soon in Strasbourg, Wolfgang Raffelsberger on behalf of the ECCB'14 local organizers [[alternative HTML version deleted]] </div

Sequencing Pathways Sequencing Pathways

updated 11.5 years ago • Wolfgang Raffelsberger

<div class="preformatted">Dear Sir/Madam I am in the process of learning how to use the easyRNAseq package for bioconductor but have a question/problem. The problem is that the organisms I am working with do not have any comprehensive genome information (or any prior sequencing) in effect I will be creating...to use the easyRNAseq package for bioconductor but have a question/problem. The p…

Annotation PROcess easyRNASeq Annotation PROcess easyRNASeq

updated 13.7 years ago • Yates, Steven A

dry and wet lab researchers, students and managers. They will be responsible for the accurate organization and curation of thousands of patients worth of genomic, administrative, experiment, and sequencing data. They...the aforementioned data. They will enact, educate and enforce data storage policies to ensure the organization of the database. They will be responsible for the resolution of e…

computational genomic big data bioinformatics Job

updated 6.5 years ago • jmaanaki

Error in file(con, "r") : cannot open the connection to 'https://www.uniprot.org/uniprot/?query=organism:9606&format=tab&columns=id' In addition: Warning message: In file(con, "r") : cannot open URL 'https://rest.uniprot.org...uniprotkb/query=organism:9606&format=tab&columns=id': HTTP status was '400 Bad Request' sessionInfo( ) R version 4.2.1 (2022-…

UniProt.ws

updated 3.4 years ago • julien.wollbrett

split(retVal[[geneID]], retVal[["go_id"]])) } ``` I created a custom OrgDb (for a non-model organism) using `AnnotationForge`, which I wanted to use with `topGO`. The custom OrgDb didn't have tables like `go_bp`, so `topGO` wouldn...and it is overwhelming at times, since it seems a lot more difficult to work with a non-model organism. It took me a long time to figure out why `split()` …

topGO AnnotationForge

updated 6.8 years ago • psutton

TRUE/FALSE needed In addition: There were 11 warnings (use warnings() to see them) > gpQuality(organism = "Hs") [1] "Starting gpQuality..." Error in if (abs(MMR[i]) > 0.5) numSpotOverMmrLim <- numSpotOverMmrLim + : missing value where...gt; traceback() 2: slideQuality(gp, controlMatrix = controlMatrix, DEBUG = DEBUG) 1: gpQuality(organism = "Hs") I changed my locale to as…

updated 11.4 years ago • Guest User

and feed it to limma/voom in order to fit a multi-factorial blocked model in a poorly annotated organism (draft genome and txome, but orthologs poorly characterized thus far). It appears to work properly in human and mouse...i.e. the top hits are reasonable); is it sensible to generalize to non-model or poorly- annotated organisms in this fashion? Probably something that could be puzzled out giv…

Transcription edgeR Transcription edgeR

updated 11.3 years ago • Tim Triche

gmane.sci...onductor/43677. Following the traceback: 1: easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", annotationMetho 2: easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", annotationMetho 3: parallelize

Organism Organism

updated 13.2 years ago • delhomme@embl.de

when you want to use biomaRt as an annotation source ## for this easyRNASeq requires the name of the organism, which circumvent the "custom" chromosome name map by-pass ## The solution is to fetch the annotation first obj <- fetchAnnotation...of warnings, ## because of the differing annotations rnaSeq <- easyRNASeq(filesDirectory="data", organism="custom", …

RNASeq Annotation Organism biomaRt easyRNASeq RNASeq Annotation Organism biomaRt

updated 13.8 years ago • delhomme@embl.de

<div class="preformatted">Hi Francesco, I've fixed a bug in easyRNASeq and made a couple of modifications to deal with novelties introduced in the IRanges and in the DESeq packages. I've just committed that whole bunch, so it will take ~2 days before a binary package is available. You can always install from SVN in the meanwhile. I've listed below the different examples you sent me in our…

RNASeq Annotation BSgenome convert biomaRt BSgenome IRanges DESeq easyRNASeq RNASeq

updated 13.8 years ago • delhomme@embl.de

m trying to perform a GO enrichment analysis using clusterProfiler. I've done this before for model organisms like human or A. thaliana for which there are annotation packages available. Now I'm struggling to do this for tomato

OrgDb Bioconductor AnnotationHub clusterProfiler

updated 4.6 years ago • ju.ry

goal, and I'm wondering if any of the available tools are suitable. I have several non-model organisms for which I've generated KEGG KO identifiers for. Instead of looking for significant differences in expression

gene set enrichment KEGG

updated 7.8 years ago • RMRG

I have downloaded data from EMBL-EBI (ArrayExpression myocardial infarction) Acession number E-MTAB-3573 raw data, cel file name (Wangyaping normal and disease condition, organism HOMO Sapiens). I have used this paper (Microarray Data Analysis for Transcriptome Profiling) command line RUN in Rstudio...Acession number E-MTAB-3573 raw data, cel file name (Wangyaping normal and disease condition, or…

oligo package

updated 6.7 years ago • cpyadav22

the whole geneList set? The code for GSEA I am using is: `kkGSEA <- gseKEGG(geneList=geneList, organism = "hsa", nPerm = 1000, pvalueCutoff = pvalue_gsea, minGSSize = 5)` Any help would be much much appreciated. Thanks :D

clusterProfiler GSEA geneList

updated 6.4 years ago • lucap

Hello Sir, I am using it for non-model organisms. 1) I have a set of differentially expressed genes, plus the go term related to genes. 2 ) The command in R in need to use

annotation goseq

updated 5.5 years ago • kumararya563

Hi, Not sure if I have mis-understood. It looks like GAGE can be used for non-model organisms using KO? I have a set of data - gene IDs with associated kegg Ids from using KAAS for my genome. geneID     &nbsp

kegg pathway analysis non-model gage pathview

updated 7.4 years ago • bekah

Hi all, I am trying to perform a GO enrichment analysis on a list of differentially expressed genes and I am having doubts on the robustness of the results. I am using the GOstats package and the organism is Apis mellifera, so I had to make a custom gene universe set, which consists of 7903 genes for which GO terms were available...and I am having doubts on the robustness of the results. I am …

GOstats GO RNASeq

updated 4.1 years ago • joasmile84

tempPerl238e1f29.pl line 6. Warning messages: 1: Built for UCSC is not valid! in: getUCSCBuilt(organism) 2: cannot open file '/tmp/RtmpQ29612/tempOut625558ec', reason 'No such file or directory' Error in if (!is.null(ug) &&amp...baseMapType = myBaseType, otherSrc = NULL, pkgName = "TIGR40K.mapGB", pkgPath = myDir, organism = "Homo sapiens", version = "1.1.0", author = my…

GO Organism annotate AnnBuilder GO Organism annotate AnnBuilder

updated 19.8 years ago • Aedin Culhane

KEGG pathways and it works perfectly for human or mouse. I am now trying to use it with a non-model organism, *Stylophora pistillata*, but which is in the KEGG organism list (see "spis" at https://www.genome.jp/kegg/catalog/org_list.html

gage

updated 6.2 years ago • mel.p

However, when I run spia, I get an error I cannot understand > res<-spia(de=de_pg, all=all, organism="mmu",beta=NULL,nB=2000,plots=FALSE, verbose=TRUE,combine="fisher") Error in spia(de = de_pg, all = all, organism = "mmu", beta = NULL

Organism limma SPIA Organism limma SPIA

updated 13.9 years ago • Moritz Kebschull

use the SPIA package, but it kept on giving me the error : "Error in spia(de = DE_top, all = ALL_top, organism = "hsa", nB = 2000, : de must be a vector of log2 fold changes. The names of de should be included in the refference array!" Would...tg1$ENTREZ) ALL_top = top$ENTREZ DE_top[1:10] ALL_top[1:10] res = spia(de = DE_top, all = ALL_top, organism = "hsa",nB = 2000, plots = FALSE, beta …

Organism limma SPIA Organism limma SPIA

updated 15.6 years ago • Barbara Bo-Ju Shih

the Stanford University School of Medicine, CA, USA! We look forward to seeing you in Berlin! The organizers and chairs of CAMDA 2013 Chairs: Joaquin Dopazo, CIPF, Spain Sepp Hochreiter, Johannes Kepler University, Austria...David Kreil, Boku University, Austria Simon Lin, Marshfield Clinic, U.S.A. Local organizer: Djork-Arné Clevert, Johannes Kepler University, Austria Contact: camda@bioinf…

Genetics Genetics

updated 12.9 years ago • CAMDA 2013

Power Platform][1] is a collection of low-code and no-code tools designed to empower individuals and organizations to create custom business solutions. It consists of four main components: Power Apps, Power Automate, Power

IntEREst

updated 2.4 years ago • John

TRUE) \#\# Not run:  \# construct lognormal background bg.logn = makeBackground(motifs, organism="dm3", type="logn

pwmenrich

updated 7.6 years ago • gdeniz

covariates: age (n=5) and phenotype (n=2, control and disease). The samples are independent (one organ per animal). I would like to evaluate time-dependent (age-dependent) between class (between phenotype) gene expression

edge timecourse fittimeseries

updated 10.1 years ago • warren.anderson

I am trying to help someone get some figures generated of some methylation data and she, who has less experience than I with R (which isn't really much) showed me trackViewer and said that the lollipop diagrams she's seen in the examples are exactly what she's is hoping to be able to generate. I started to look at the trackViewer documentation but it isn't clear to me if we can use our own genomi…

trackViewer

updated 6.1 years ago • martinson.john

for doing DE analyses outside of trinity. I am working with a de novo assembly from a non-model organism (2 genotypes) and I don't have a high quality genome assembly to go with it. I have carried out transcript-level abundance

tximport salmon rna seq de novo

updated 7.2 years ago • RMRG

Hi I'm trying to ues retrieveKGML from KEGGgraph package: retrieveKGML(pathwayid="05211", organism="hsa", destfile=tmp) Warning message: In download.file(kgml, destfile = destfile, method = method, ...) : download had nonzero

KEGGgraph KEGGgraph

updated 15.0 years ago • Yan Jiao

house and public transcriptomic datasets and creating tools to improve data accessibility across the organization. Contributing across the breadth of ongoing research programmes. From a technical perspective, ideal candidates

Transcriptomics Bioconductor Statistics Job Biocon

updated 4.8 years ago • m.jackson

div class="preformatted">Hello, I have ~100 RNA seq-samples from the same organism, but they include different experiments (each experiment of 6-16 samples). I would like to put all together into our

Normalization Organism DESeq Normalization Organism DESeq

updated 11.6 years ago • Guest User

https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/819/885/GCF_009819885.2_bCatUst1.pri.v2/", organism = "Catharus ustulatus")) Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame...source: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/819/885/GCF_009819885.2_bCatUst1.pri.v2/ Organism: Catharus ustulatus Taxonomy ID: 91951 miRBase build ID: NA Gen…

GenomicFeatures

updated 3.0 years ago • oluwamosope

Now when I run spia, I get the following error: > res <- spia( de=DE_gr_iii, all=ALL_gr_iii, organism="mmu", nB = 2000, plots=F, beta=NULL ) Error in spia(de = DE_gr_iii, all = ALL_gr_iii, organism = "mmu", nB = 2000, : de must be a vector of log2...de_ttt ) <- all_ttt The result was, again, error: > res <- spia( de=de_ttt, all=all_ttt, organism="mmu", nB …

Microarray GO Cancer Organism hgu95av2 mgug4122a SPIA Microarray GO Cancer Organism

updated 15.6 years ago • January Weiner

The size of my gene set is = 364): Enrich\_Hr1.2\_1 <- enrichPathway(FC\_Hgr1.2$\`Entrez ID\`, organism = "mouse",                               readable = F, pvalueCutoff = 0.05,&nbsp...nbsp;     maxGSSize = 500__) Enrich\_Hr1.2\…

reactomepa pathway analysis enrichment analysis clusterprofiler

updated 8.1 years ago • Miguel.Cosenza

related to a specific epigenetic modification (H3K4me3), under different development stages of the organism that I'm working with (a fungus), and with different strains (genotypes) of it. I would like to produce PCA (Principal Component

ChIPseqR

updated 18 months ago • egbastakis

ID's like the ones i have? I take those ID's from the NCBI GAFfile of the reference genome of my organism (Hydractinia symbiolongicarpus) ```r [1] "PANTHER:PTN000900048" "PANTHER:PTN001039662" "PANTHER:PTN001559200" [4] "PANTHER

PANTHER.db

updated 21 months ago • nromerov

I am trying to do a GO enrichment analysis using ClusterProfiler. I am working with an unsupported organism, so I am supplying my own GO terms with the functionTERM2GENE. However, I am getting an error message. ``` ego_bp_aga &lt

clusterProfiler DESeq2

updated 3.5 years ago • Lucía

set in standard Affymetrix CEL-format consisting of only six samples without any replicates (same organism and cell type, but different individuals and different biological conditions for each individual; the same Affymetrix

Microarray Clustering Microarray Clustering

updated 16.2 years ago • Rainer Tischler

head(gene) ego <- enrichGO(gene = gene, universe = names(geneList), organism = "human", ont = "CC", pAdjustMethod = "BH", pvalueCutoff = 0.01, qvalueCutoff = 0.05, readable = TRUE) head(summary(ego)) cnetplot(ego

clusterProfiler DOSE

updated 10.0 years ago • Vinicius Henrique da Silva

Hello, I am PhD student and im working on a non-model organism trying to understand the differences in expression patterns and differentially expressed genes between resistant

rnaseq differential gene expression

updated 8.2 years ago • laksharikrish

structure takes ca. 2 seconds. I'm pretty sure there is more essential processing done by getGEO to organize the data into a GSE object, but still, there seems to be an incredibly inefficient implementation underneath. I haven

GEOquery GEOquery

updated 16.6 years ago • Wacek Kusnierczyk

p/61581/#61641)[ ](#) I explain here in more detail my problems with the creation of an organism package. I tried to create my orgnaism package using the function [makeOrgPackage() ](http://bioconductor.org/packages...goTable=go)</pre>   The creation was succesfull and I have the following organism package now:   <pre> > ls("package:org.Psp.FOBEG1.eg.db…

organismdb annotationdbi annotationforge

updated 11.2 years ago • artur

<div class="preformatted">Hi Asis, So to get the most thorough answers to questions about bioconductor, please post them here at the official bioconductor list. The core team is a small group and we can't possibly presume to know as much as the 3000 other bright and talented people who subscribe to our list. ;) Answers to your questions: 1) GOALLFrame has many annotations because it is …

Annotation GO Organism AnnotationDbi Annotation GO Organism AnnotationDbi

updated 12.2 years ago • Marc Carlson

I am using the attached biomart script for calculating the dn/ds ratio's between the human and model organisms. However, in an output file, I am getting dn/ds ratios only for mouse and rat. For the rest of the model organisms (worm

biomaRt

updated 4.0 years ago • morgantom1221

<div class="preformatted">Dear Mark, I'm cc'ing the Bioconductor mailing list in case it helps others. I've implemented the support for variable read length (version 1.3.7 of easyRNASeq, available in SVN now and in a couple of days from Bioc). Thanks for your reproducible use case. Below is the code I ran: library(easyRNASeq) counts <- easyRNASeq(organism="Dmelanogaster", …

Annotation Organism BSgenome convert BSgenome easyRNASeq Annotation Organism BSgenome

updated 13.5 years ago • delhomme@embl.de

to someone soon! -Lola ```st <-clusterProfiler::compareCluster(genes, fun = "enrichKEGG",organism="dre",pvalueCutoff=0.05) ```st <- clusterProfiler::setReadable(st, "org.Dr.eg.db", keyType = "ENTREZID") **Error in .testForValidKeys

clusterProfiler

updated 3.4 years ago • ltb47

<div class="preformatted">Dear list, I'm working on a custom chip from Roche Nimblegen, I perform to create an Annotation package for "pd.110916.mtub.h37rv.im.exp.til" built with pdInfoBuilder, and I 've identified some DEG's. Now I would like to do Gene Ontology and GSEA with these genes.I know I have to use these library(GOstats); library(GO.db); library(annotate)but I miss library(my_o…

Annotation Organism PROcess Annotation Organism PROcess

updated 13.1 years ago • Ingrid Mercier

enriched pathways.  <pre> rpa <- enrichPathway(gene=geneSS, pvalueCutoff=0.05, readable=T, organism="pig") head(as.data.frame(rpa)) [1] ID Description GeneRatio BgRatio pvalue p.adjust [7] qvalue Count <0 rows> (or 0-length

reactomepa clusterprofiler

updated 7.8 years ago • thomasjenner333

makes the reasonable but flawed assumption that Ensembl will only add, not remove, organisms from its current\_mysql directory. _Agambiae_ was removed from the main ensembl site when it was moved to the metazoa

genomicfeatures

updated 8.5 years ago • matt.chambers42

selected to calculate the back ground model, also be promoter sequences of the same(and of the same organism)probes? Thanking you in anticipation. Regards, Prashantha ###################################################################### Attention: This e-mail message is privileged and confidential

probe cosmo probe cosmo

updated 15.8 years ago • Prashantha Hebbar Kiradi [MU-MLSC]

stored in 6 tables (BP, BP_all, MF, MF_all, CC, CC_all) looking like the format that I found for the organism packages in BioC: ID GOID evi 6092 GO:0000910 IEA 6092 GO:0040035 IEA 6092 GO:0000398 IEA So if someone could help me

Annotation GO Organism Annotation GO Organism

updated 13.2 years ago • Fabian Grammes

Exp. Genes pvalue: 0.00110121111270826 total genes from chip : 16 [2] GO:0030199 collagen fibril organization 2 Genes associated out of my differ. Exp. Genes pvlaue: 0.0929493556475916 total genes from chip : 14 GOHyperG

GO GO

updated 20.8 years ago • SAURIN

targets, basically it would be a mapping between Entrez Gene IDs and miRNA families, for a couple of organisms, together with some additional info or course. I am trying to make use of the AnnBuilder package, but could not find

miRNA Annotation AnnBuilder miRNA Annotation AnnBuilder

updated 16.9 years ago • Gábor Csárdi

arrays we're working with seem to have fewer genes on them than the total number cataloged in the organism's online databases. So should m and n be based on the absolute total number of genes annotated, or the number of genes

GO GOstats GO GOstats

updated 19.6 years ago • Jacob Michaelson

but first need to have a GDS file prepared by snpgdsBED2GDS. I'm working with a nonmodel organism that has 19 autosomes and over 1000 scaffolds which are not assigned to any autosome. Interestingly, my GDS files

GENESIS GWAS GDS

updated 7.2 years ago • naglemi

but I still do not know how to proceed. I have a series of experiments performed on a single organism which include experiments like: comparing antibiotic sensitive and antibiotic resistant strains, comparing

limma deseq2 normalization degenes design and contrast matrix

updated 8.4 years ago • mrigaya.mehra

Hi, how is the "binding/association" tag handled, when a xml is parsed to a graph object in R? E.g. for the entry <relation entry1="47" entry2="53" type="PPrel"> <subtype name="binding/association" value="---"/> </relation> I get an arrow from 47 to 53. However, shouldn't it be bidirectional, because the direction is not k…

kegggraph

updated 8.3 years ago • Martin Pirkl

_3.0.5 on R  3.3.1  as follows : <pre> kegg <- enrichKEGG(entrez_id, organism="hsa", pvalueCutoff=0.05, pAdjustMethod="BH", qvalueCutoff=0.2,use_internal_data=FALSE) write.csv(summary(kegg),file

clusterprofiler qvalue

updated 9.1 years ago • ZheFrench