Bioconductor Forum

hello I am a beginner who just started using rstudio (I just know how to make a Venn diagram in R). I tried to create a GO plot using usegalaxy, but they did not provide detailed plots for CC, BP, and MF (probably because my organism is not a widely known organism such as human or mouse). I have a goseq result file annotated as below. Is there anyone who can give me some help or com…

clusterProfiler ggpubr

updated 19 days ago • BCS12

I am suddenly having trouble using goseq for supportedOrganisms as bioconductor suddenly seems unable to retrieve the appropriate data from the UCSC database

goseq Bioconductor rtracklayer

updated 7 weeks ago • thomas

HI, I'm getting following warning from `nullp` function from `goseq` package. ``` pwf=nullp(gene.vector1, bias.data=length.vec) Komunikat ostrzegawczy: W poleceniu 'pcls(G)': initial point very

goseq

updated 12 weeks ago • boczniak767

I am trying to install "goseq" Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2...I am trying to install "goseq" Bioconductor package in Rstudio (version- RStudio 2022.07.2 Build 576 ) on my system I have installed R version- 4.2.2 I getting many error messages which are the following please help me. ``` * installing *source* …

R Bioconductor Install

updated 17 months ago • abhisek001

Hi I have a list of differentially expressed genes for E.coli (BL21). Now with this genes I would like to do some downstream analysis. Can you guys help me out with some ideas? I tried to do some functional enrichment analysis but I dont have any ENTREZ id. How can I tackle this problem

DESeq2 GO goseq FunctionalAnnotation

updated 17 months ago • acram

Hi, I am trying to do GO enrichment analysis. I work on Cannabis sativa, which is a non-model organism. There are no GO terms for Cannabis, so I cannot make use of the orgdb or biomart functions in R. However, I have generated a file with GO terms mapped to protein id from the original fasta. My file looks like this: ```r !db db_object_id db_object_symbol qualifier …

clusterProfiler goseq topGO DESeq2

updated 23 months ago • Lucía

I've found myself in the situation where goseq fails with some relatively extreme numbers (derived from ChIP-Seq data with extreme changes in the IP target) and have

goseq

updated 24 months ago • Steve Pederson

cruk-summer-school-2018/RNASeq2018/html/06_Gene_set_testing.nb.html#go-enrichment-analysis in the goseq package. The code to make this plot taken from the site is the following: ```r goResults %>% top_n(10, wt=-over_represented_pvalue...in the R documentation. Will the way I have written the plot give an analogous output as the goseq package? The output from gage is p.geomean,stat.me…

gage plot RNASeq goseq

updated 2.1 years ago • m.glymenaki

to do a GO term enrichment analysis. How may I get the GO term for all of my genes using R package "goseq". I haven't found the database for soybean genome in bioconductor. Also online software like DAVID, shinyGo is not recognizing

GOTerm

updated 2.1 years ago • Afsana

pathway analysis. I have used the gage package and I was looking online about another package called goseq that takes into account length bias. However, when I run the code I get an error. How to solve that as I am not sure what the...error means? ```r library(goseq) supportedOrganisms() %>% filter(str_detect(Genome, "hg")) #Step 1 #prepare the results for goseq de.genes&am…

Pathways goseq RNASeqData

updated 2.1 years ago • m.glymenaki

of package ‘minfi’ had non-zero exit status 31: In .inet_warning(msg) : installation of package ‘goseq’ had non-zero exit status 32: In .inet_warning(msg) : installation of package ‘methylumi’ had non-zero exit status 33: In .inet_warning

newpackage ChAMP

updated 2.5 years ago • Brendon

I am trying to make an organism db to use with GoSeq for pancium hallii. Using the biomart package I found what dataset to use but I get the error that 0 or more than 1 subdir

FunctionalAnnotation

updated 2.9 years ago • Catherine

a few other related packages, I think). However, I've carried out GO/KEGG enrichment analyses using GOSeq so I can account for any potential sequence length biases. Is there a way to to use the various plotting functions with...data from other programs like GOSeq? Can we convert the results into the format required for ```emapplot()``` etc? The results for GOSeq, at least, are just stored in

clusterProfiler enrichplot

updated 3.0 years ago • charles.foster

which are ensembl Ids I wanted do GO analysis for this list of genes. How can I do this from the GOseq I went through vignette which is running the GOseq from the DE genes output, my genes list are not from the DE this are obtained

goseq

updated 3.1 years ago • Lucky

I am using goseq to run analysis on my RNA seq data. Previously it had worked for me, but recently, I am encountering an error when trying...I am using goseq to run analysis on my RNA seq data. Previously it had worked for me, but recently, I am encountering an error when trying to load the package. The error reads as ```r > library(goseq) Loading required package: BiasedUrn Loa…

DESeq2 goseq

updated 3.2 years ago • avinashi

I'm getting a warning message when I try to run Gene Ontology analysis with *goseq* using human genome assembly GRCh38 (hg38). I know that hg38 isn't natively supported by *goseq*, but *goseq* will fetch *goseq...installed. Thus, I run the following code: ``` library(TxDb.Hsapiens.UCSC.hg38.knownGene) library(goseq) # load toy dataset aa = c(1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,1,1) names(aa) …

goseq

updated 3.2 years ago • Nikolay Ivanov

reads were mapped to the genome build/version `sacCer3`. sacCer3 was released in 2014. I've tried `goseq`, which has built in support for sacCer2 but not sacCer3 (oy vey!). I was able to run my dataset using sacCer2, but **are GO Annotations...for sacCer2 in goseq up to date**? I've tried to make my own genome/object for use with goseq. I have a vector of gene names and lengths, but I canno…

clusterProfiler AnnotationDbi OrgDb goseq

updated 3.2 years ago • vanbelj

Hi, I have done differential expression analysis with `DESeq2`. With `goseq` I can see there are pathways of interest differentially expressed- that makes sense to our biological observations

roast DESeq2 GeneSetEnrichment

updated 3.4 years ago • prabin.dm

dds <- DESeq(ddsMat,betaPrior=TRUE) res <- results(dds) # Extract results library(goseq) genes=as.integer(p.adjust(res$pvalue[res$log2FoldChange!=0], method="BH")<.05) names(genes)=row.names(res[res$log2FoldChange...pwf=nullp(genes,"hg38","ensGene") head(pwf) ``` ![Error message for GO terms analysis with goseq][1] [1]: /media/images/Capture_kzNEGwU.JPG

KEGG Pathways GO goseq

updated 3.4 years ago • ojong

Hello, I'm working recently on GO analysis regarding A.thaliana whose database is not included in GOseq package. Then I downloaded the GO annotation from both gene ontology website and TAIR as DAF file (version 2.0/2.1) and

goseq rnaseq r

updated 3.5 years ago • citronxu

TA GO:0016616 BGIOSGA013239 BGIOSGA013239-TA GO:0051287 ..................... Goseq code: d <- read.csv("deseq2res.csv", header=T, row.names=1) all_genes <- row.names(d) DE_genes <- all_genes[d$padj<0.05...head(pwf) # calculate GO enrichment using default method GO.WALL <- goseq(…

goseq

updated 3.7 years ago • nabiyogesh

Hello I am using go-seq for gene enrichment study. I am having few confusion I will be very grateful if I can get some help. 1) I know we need gene length to calculate the bias. 2) I want to do gene enrichment of two groups compared to the control group. - i got a list of transcripts which are commonly differential expressed in both theses group(A, B) against the control group. - …

goseq

updated 3.8 years ago • kumararya563

Hello -I am using Go-seq for my gene enrichment study. - I have my pwf test file which look like below. This file has protein ID as row names. - My question in order to do mapping between the two files, do I need to select column from the GAF format file. and then split the column, to get the protein id name so that I can further do mapping. Looking forward to hearing, and thanks for …

goseq

updated 3.8 years ago • kumararya563

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 is: goseq(pwf, genome, id, gene2cat = Null) I understand that for gene2cat argument I need to mention my list of genes with their go term.Correct...expressed genes, plus the go term related to genes. 2 ) The command in…

annotation goseq

updated 3.9 years ago • kumararya563

Hi, I've performed gene ontology analysis with GOseq using the standard ontologies, as well as using KEGG and Reactome. When using the default ontologies or KEGG, the function

goseq go rna-seq

updated 4.1 years ago • hasse.bossenbroek

is running Debian 10 with the default version 3.5.1 of R. I need to use the Bioconductor package "GoSeq" to perform functional enrichment tests as described in “Running GOSeq” pipeline (https://github.com/trinityrnaseq/trinityrnaseq...wiki/Running-GOSeq). I got a trouble with it. The package "GoSeq" exists only for “R version "3.6" in Bioconductor Release 3.10 which works with...https://communi…

goseq installation

updated 4.3 years ago • gdalsky

was also performed through the analyze_diff_expr.pl script. The function calls the R package **goseq**, and [as stated here][2], the output looks this way: *Two outputs will be generated for each set of genes tested for functional...Trinity-Differential-Expression [2]: https://github.com/trinityrnaseq/trinityrnaseq/wiki/Running-GOSeq [3]: https://i.ibb.co/WDvmhxb/41390-2018-192-Fig3-HTML…

go enrichment gene ontology goseq go

updated 4.6 years ago • Raito92

Hello, I've tried to install the package goseq with: if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("goseq") But...R/library/geneLenDataBase’ ERROR: dependency ‘geneLenDataBase’ is not available for package ‘goseq’ * removing ‘/usr/local/lib64/R/library/goseq’ The downloaded source packa…

goseq r package r

updated 4.6 years ago • Raito92

Dear all, I have carried out differential expression of RNA-seq data from a non-model organism using the limma+voom pipeline. Next, I wish to look for functional enrichment of DE genes using GOseq. I successfully used GOseq on my data set by following the GOseq vignette, using custom gene lengths and GO mappings. However, I note that following the vignette leads to **all** DE genes being t…

goseq

updated 5.0 years ago • charles.foster

Hello there, I have a question concerning usage of GOseq for testing custom gene list (approx. 1k genes) enrichment. I am not sure about the `use_genes_without_cat` argument value

goseq

updated 5.2 years ago • kubovcij

I did the GO terms enrichment analysis using GOSeq, after that I want to access the esIDs in the significantly enriched terms. I tried to extract esIDs using `` org.Hs.eg.db...in `` GO.wall `` report is 124, so is there any method to directly access the genes in GO terms in GOSeq

GOseq ensemblid GO

updated 5.5 years ago • mico

out (high scatter, poor fit). I have seen quite a few of these graphs when searching for "pwf plot goseq" on google including some on the bioconductor forum - but as yet there is no explanation for this.   Any ideas why this

goseq

updated 5.5 years ago • Jakub

I am using goseq for category testing of differentially expressed genes in my RNA-seq data sets and I wanted to extend it to categories...I am using goseq for category testing of differentially expressed genes in my RNA-seq data sets and I wanted to extend it to categories other than the GO categories. Specifically, I wanted to make use of the molecular signatures database (MSigDB). To be clear, …

goseq category test

updated 5.6 years ago • Mthabisi Moyo

over representation) analysis of GWAS/QTL data distributed over a genome, is it possible with goseq?  I could not find any useful tutorials/manual -- could someone kindly show (1) required inputs (format, etc.; e.g. we have...coordinate locations", "a small segments of a genome region to test"), (2) command line to run R/goseq (so that we can build a pipeline to run as routine), and (3) …

goseq enrichment GWAS

updated 5.7 years ago • zhu

nbsp; Dear all, I am running GOseq on a custom annotated dataset. I am getting a nicely looking output: list of enriched and depleted GOterms for my different

GOseq GO pwf goseq

updated 5.7 years ago • TB18

using Trinity and RStudio and I am very new to all of this. I have a problem with the output of goseq. I get many GO terms in each category instead of getting one go term per category which is what I see in every paper. I believe...GO:1902494" "GO:1903046" "GO:1903293"</p> </td> </tr> </tbody> </table>     GO.wall=goseq(pwf, gene2cat = geneID2GO, …

go goseq goterm category

updated 5.7 years ago • Juan

Hi, The number of genes in a GO geneset determined by goseq is different from what I obtained by querying org.Hs.eg.db. I ran the following: <pre> library(goseq) data(genes) pwf.eg...nullp(genes,"hg19","ensGene") GO.wall.eg=goseq(pwf.eg,"hg19","ensGene", test.cats='GO:BP') head(GO.wall.eg,5)</pre> It shows that GO:0000278 is top candidate and has 922 for numInCat

goseq

updated 5.7 years ago • siajunren

Hi I am trying to build the organism package for sheep. At the first i used the codes that was in vignette help page. and so run makeOrgPackage. makeOrgPackage(gene\_info=fSym, chromosome=fChr, go=fGO, version="1.0.0", maintainer="Some One <so@someplace.org>", …

goseq

updated 5.8 years ago • Mehdi

Hi All, I am using GOseq as part of the Trinity pipeline to perform gene ontology testing for genes in a _de novo_ transcriptome assembly...Hi All, I am using GOseq as part of the Trinity pipeline to perform gene ontology testing for genes in a _de novo_ transcriptome assembly. I used edgeR to perform DGE analysis comparing groups that were treated with a che…

goseq go enrichment

updated 5.8 years ago • mart1139

Hi everyone, I’m testing for GO categories enrichment using goseq (version 1.32.0) under two different approaches (as described below) and I’m getting different numbers of genes per GO...without categories in the test, the number of genes per category is the same! <pre> > GO.hiper = goseq(pwf, "bosTau4", "ensGene", use_genes_without_cat = TRUE) > GO.hiper[GO.hiper$category…

goseq biomart

updated 5.9 years ago • frezende

I am running GOseq for mouse data using ~800 genes as input and ~8K genes as background lists.  Running GOseq I get the same number of enriched

goseq

updated 5.9 years ago • sharvari gujja

I maintain "rgsepd" which uses "DESeq2" and "goseq" to run an annotation pipeline. Internally, when I have a character representation of a GO term I'm interested in more...I maintain "rgsepd" which uses "DESeq2" and "goseq" to run an annotation pipeline. Internally, when I have a character representation of a GO term I'm interested in more information

GO.DB

updated 6.0 years ago • karl.stamm

Hi, I was having much trouble trying to install a goseq database in the annotation section. source("https://bioconductor.org/biocLite.R")   biocLite("org.Mm.eg.db") This...Hi, I was having much trouble trying to install a goseq database in the annotation section. source("https://bioconductor.org/biocLite.R")   biocLite("org.Mm.eg.db") This was...BiocInstaller 1.28.0)…

goseq org.hs.eg.db

updated 6.1 years ago • nancyjwahl7

I’m trying to run GOSeq with human RNA Seq data that has been processed with Salmon, summarized to gene level with tximport, and DGE run using...DeSeq2.  I was reading the vignette for GOSeq and got stuck/confused on the part where you need to know what human genome build you used... It says you need to know this...genome, correct? So then could I just use the avgTX length from the txim…

deseq2 tximport goseq

updated 6.1 years ago • casey.rimland

C stack usage  7969392 is too close to the limit ERROR: lazy loading failed for package ‘goseq’ \* removing ‘/home/biosys5/R/x86\_64-pc-linux-gnu-library/3.4/goseq’ The downloaded source packages are in     ‘/tmp...message: In install.packages(pkgs = doing, lib = lib, ...) :   installation of package ‘goseq’ had non-zero exit status So…

go

updated 6.1 years ago • TB18

Hello everyone, I am new to this forum so I'm apologizing in advance if I am not posting in the most formal way. I am using the goseq package from bioconductor in order to perform enrichment for markers that are differentially methylated (limma output). These markers have been measured  according to CpG arrays from 450K illumina (i.e. cg07790169) and I am retrieving them on uc…

goseq methylation ensembl ucsc limma

updated 6.1 years ago • dusan.petrovic

managed to test for differential gene expression using "DESeq2" followed by GO-analysis with "goseq". So far, so good. However, I would like to know which genes (annotated to this pathway) are differentially expressed in my...dataset.   <pre> library(DESeq2) library(goseq) library(GO.db) library (org.Mm.eg.db) library(annotate)</pre> <pre> #"DESeq2": Pulling …

deseq2 goseq rnaseq go enrichment differential gene expression

updated 6.2 years ago • josef.oeckl

Recently, I have tried to apply GOSeq to RNA-seq expressions after voom adjustment. It has just ocurred that differential expression and gene length were

limma limma-voom goseq

updated 6.2 years ago • joelrosa

Hi all,   I am trying to install goseq as specified [here. ](https://bioconductor.org/packages/release/bioc/html/goseq.html) This is the commands I put in: R source...https://bioconductor.org/biocLite.R") biocLite("goseq") At the end of the installation, it prints this: The downloaded source packages are in       &n…

goseq installation

updated 6.4 years ago • philipp.voss

Hi, I'm trying to use PANTHER.db to conduct pathway analysis on a set of differentially expressed genes, and I'm running into an error when loading PANTHER. I install as usual:

biocLite("PANTHER.db")
library(PANTHER.db)

But when I type PANTHER.db at the console, I obtain the following error:

Error in rsqlite_send_query(conn@ptr, statement) :
  external pointer is not valid

This e…

goseq pantherdb pathway analysis gene ontology

updated 6.4 years ago • krc3004

I have successfully conducted a gene ontology analysis using goseq. In presenting the findings of the analysis (i.e., the standard output generated by the \`goseq\` function) to a colleague, he...function were those associated with any given significant GO or KEGG term arising as output of the \`goseq\` function. The columns \`numDEInCat\` and \`numInCat\` clearly summarize this information (i.e…

goseq gene ontology

updated 6.5 years ago • JMallory

Hi, On 02.01.2017, I ran an analysis with DESeq2. I ran a similar analysis recently. I used the same input data for both runs! Please see "raw reads" in the excel file ([https://www.dropbox.com/s/g7fyqvn1chdnesh/deseq2\_bugreport\_23102017.xlsx?dl=0](https://www.dropbox.com/s/g7fyqvn1chdnesh/deseq2_bugreport_23102017.xlsx?dl=0)). Even tough the normalized reads and basemean are same in both runs…

deseq2

updated 6.5 years ago • Mehmet Ilyas Cosacak

Hello I got this error when using supportedGenomes() in goseq package: <pre> > library(goseq) Loading required package: BiasedUrn Loading required package: geneLenDataBase > head

goseq rtracklayer

updated 6.5 years ago • mgdrnl

I am trying to run goseq package in R, working with human data with hg19. I followed the vignette instructions to create "gene.vector", but I am...I am trying to run goseq package in R, working with human data with hg19. I followed the vignette instructions to create "gene.vector", but I am getting

goseq GO term

updated 6.6 years ago • pereyra.s

nbsp; Anyone has some advice on how to get it running?  Thank you,   > library(goseq) Indlæser krævet pakke: BiasedUrn Indlæser krævet pakke: geneLenDataBase Error: package or namespace load failed...goseq’ in loadNamespace(j <- i\[\[1L\]\], c(lib.loc, .libPaths()), versionCheck = vI\[\[j\]\]):  der er ingen pakke med navn ‘GO.db’ > so…

GO.db goseq package installation error

updated 6.6 years ago • veerle

f1000research.com/articles/5-1438/v2) until _Pathway analysis_ because I wanted to replace it by `` goseq ``. > head(gene_len) V1 V2 V3 1 Length GC NA 2 sp0000001 6406 0.3535748 3 sp0000002 333 0.5495495 4 sp0000003 216 0.4583333

edger goseq

updated 6.6 years ago • mictadlo

#!/usr/bin/env Rscript # based on https://www.biostars.org/p/84467/#84495 # source("https://bioconductor.org/biocLite.R") # biocLite("GenomicRanges") # biocLite("rtracklayer") biocLite("Rsamtools") library(GenomicRanges) library(rtracklayer) library(Rsamtools) GFFfile = "Sp.gff" FASTAfile = "Sp.faa" #Load the annotation and re…

goseq

updated 6.6 years ago • mictadlo

Hi, I found the below code [here](https://www.biostars.org/p/84467/#84495): > library(GenomicRanges) > library(rtracklayer) > library(Rsamtools) Loading required package: Biostrings Loading required package: XVector > > GFFfile = "snap_augustus.gff" > FASTAfile = "genome_29155.faa" > > #Load the annotation and reduce it …

GenomicRanges rtracklayer goseq

updated 6.6 years ago • mictadlo

I have followed this [tutorial](https://f1000research.com/articles/5-1438/v2) for edgeR. On this [side](https://toolshed.g2.bx.psu.edu/repository/display_tool?repository_id=f599adf23b671cad&tool_config=%2Fsrv%2Ftoolshed%2Fmain%2Fvar%2Fdata%2Frepos%2F002%2Frepo_2703%2Fgoseq.xml&changeset_revision=ade933eff007) it appears I could run `` goseq `` when I have created the following fil…

edger goseq

updated 6.6 years ago • mictadlo

sum(exonBaseMean), sig = max(sig) ) %>% ungroup() I can then run goseq using  the lengths as the bias data: genes <- retained_genes$sig names(genes) <- retained_genes$gene_id bias.data...CY9MhRQ.png) And then proceed to test for category enrichment: go.retainted.length <- goseq(pwf, genome='hg19',…

goseq dexseq

updated 6.7 years ago • i.sudbery