Showing : goseq • reset
1
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2
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229
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supportedOrganisms() in goseq producing Error in names(trackIds)
goseq Bioconductor rtracklayer
5 weeks ago thomas • 0
1
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4
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402
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goseq, warning and strange plot from nullp
goseq
11 weeks ago • updated 10 weeks ago boczniak767 ▴ 720
0
votes
1
reply
581
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Downstream analysis with Differentially Expressed Genes
DESeq2 GO goseq FunctionalAnnotation
updated 17 months ago by ▴ 10 • written 17 months ago by • 0
0
votes
5
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1.9k
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GO enrichment with non-model organism, supplying GO mappings
clusterProfiler goseq topGO DESeq2
updated 22 months ago by 65k • written 22 months ago by ▴ 10
0
votes
2
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822
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goseq: Wallenius Vs Fisher's Noncentral Hypergeometric Distribution
goseq
24 months ago • updated 23 months ago Steve Pederson ▴ 170
0
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0
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736
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
1
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2
replies
801
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Pathway analysis of RNAseq data using goseq package
Pathways goseq RNASeqData
2.1 years ago m.glymenaki • 0
1
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10
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2.4k
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How to run Goseq for list of ensembl gene IDs
goseq
3.1 years ago • updated 3.0 years ago Lucky • 0
1
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4
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1.4k
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goseq package loading issues
DESeq2 goseq
3.1 years ago avinashi • 0
3
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9
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1.9k
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Warning message when performing Gene Ontology analysis with goseq using hg38
goseq
updated 3.2 years ago by 65k • written 3.2 years ago by • 0
2
votes
3
replies
1.6k
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Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 30
2
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2
replies
1.1k
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Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.4 years ago by 65k • written 3.4 years ago by • 0
0
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1
reply
888
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non-native GO annotation cannot be successfully introduced into Goseq
goseq rnaseq r
updated 3.5 years ago by 65k • written 3.5 years ago by • 0
0
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0
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467
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go seq related help, where I need to do mapping between go term and the protein -id
goseq
3.8 years ago kumararya563 • 0
0
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2
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700
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Goseq_analysis related help
goseq
3.8 years ago kumararya563 • 0
1
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2
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879
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GOSeq analysis in rice
goseq
3.8 years ago • updated 3.7 years ago Jitendra ▴ 10
3
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2
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1.1k
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Goseq analysis related help.
annotation goseq
updated 3.8 years ago by ★ 13k • written 3.8 years ago by • 0
0
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0
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819
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How to identify differentially expressed genes from Reactome pathways enriched according to GOseq?
goseq go rna-seq
4.0 years ago hasse.bossenbroek • 0
4
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5
replies
1.7k
views
Downgrading R to 3.6.0 version (GOseq problem)
goseq installation
4.3 years ago gdalsky ▴ 40
0
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1
reply
2.1k
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GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment gene ontology goseq go
4.6 years ago Raito92 ▴ 60
2
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6
replies
1.1k
views
Can't install GOSEQ (dependency problem) on CentOS 7!
goseq r package r
updated 4.6 years ago by ★ 6.5k • written 4.6 years ago by ▴ 60
1
vote
1
reply
1.3k
views
GOseq analysis with only upregulated or downregulated genes
goseq
updated 5.0 years ago by ▴ 310 • written 5.0 years ago by ▴ 160
2
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2
replies
1.0k
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Using GOseq for custom gene set enrichment test
goseq
updated 5.2 years ago by 50k • written 5.2 years ago by • 0
2
votes
2
replies
2.8k
views
How to access gene IDs associated with GO terms in GOSeq
GOseq ensemblid GO
updated 5.4 years ago by 65k • written 5.4 years ago by • 0
1
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3
replies
1.8k
views
goseq: Formatting category list for use with goseq
goseq category test
updated 5.6 years ago by 65k • written 5.6 years ago by ▴ 30
0
votes
0
replies
862
views
how to: enrichment (over representation) analysis of GWAS/QTL data distributed over a genome with GOSEQ
goseq enrichment GWAS
5.7 years ago zhu • 0
0
votes
1
reply
1.2k
views
GOseq output but strange warning message!
GOseq GO pwf goseq
5.7 years ago TB18 • 0
1
vote
1
reply
1.2k
views
Goseq output with too many GO terms per category
go goseq goterm category
updated 5.7 years ago by 50k • written 5.7 years ago by • 0
3
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2
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999
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numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
goseq
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
1
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9
replies
2.1k
views
Using goseq with unsupported organism
goseq
updated 5.8 years ago by 65k • written 5.8 years ago by • 0
0
votes
0
replies
924
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GOseq No Underrepresented Categories
goseq go enrichment
5.8 years ago mart1139 • 0
8
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10
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1.6k
views
Genes listed in GO categories
goseq biomart
updated 5.8 years ago by 50k • written 5.9 years ago by • 0
0
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2
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865
views
goseq with hypergeometric method
goseq
updated 5.9 years ago by 50k • written 5.9 years ago by ▴ 40
0
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0
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1.3k
views
I finally solved my problem with installing "org.Hs.eg.db"!
goseq org.hs.eg.db
6.0 years ago nancyjwahl7 • 0
2
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6
replies
2.0k
views
Can Tximport average transcript length be used for GOSeq?
deseq2 tximport goseq
6.1 years ago casey.rimland ▴ 150
0
votes
6
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1.4k
views
How to link methylation code from UCSC (hg19-cg07790169) to ENSEMBL genome code (goseq procedure)
goseq methylation ensembl ucsc limma
6.2 years ago • updated 6.1 years ago dusan.petrovic • 0
0
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2
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3.6k
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DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 6.2 years ago by 41k • written 6.2 years ago by • 0
0
votes
3
replies
1.2k
views
What is the impact of using GOSeq to voom-adjusted RNA-seq Expressions ?
limma limma-voom goseq
updated 6.2 years ago by 50k • written 6.2 years ago by • 0
0
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1
reply
2.6k
views
installation of package 'goseq' had non-zero exit status
goseq installation
updated 6.4 years ago by 25k • written 6.4 years ago by • 0
0
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1
reply
1.6k
views
PANTHER.db- external pointer error
goseq pantherdb pathway analysis gene ontology
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 10
1
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2
replies
2.9k
views
GOseq: Determining ENSG IDs Associated with Genes Summarized by `numDEInCat` for Each Ontology Term
goseq gene ontology
updated 6.5 years ago by 65k • written 6.5 years ago by • 0
0
votes
1
reply
1.2k
views
Error: subscript out of bounds when using ucscGenomes() and supportedGenomes() functions in goseq and rtracklayer packages respctively
goseq rtracklayer
6.5 years ago mgdrnl • 0
2
votes
3
replies
1.7k
views
GOseq error on running nullp
goseq GO term
updated 6.5 years ago by 50k • written 6.5 years ago by • 0
0
votes
1
reply
2.0k
views
GO.db won't install for using goseq package
GO.db goseq package installation error
updated 6.6 years ago by 25k • written 6.6 years ago by • 0
0
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2
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1.6k
views
bias.data vector must have the same length as DEgenes vector!
edger goseq
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 10
0
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0
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1.2k
views
gene length file for GOseq
goseq
6.6 years ago mictadlo ▴ 10
2
votes
2
replies
1.4k
views
Error in normSplitFactor(f, x)
GenomicRanges rtracklayer goseq
updated 6.6 years ago by ★ 11k • written 6.6 years ago by ▴ 10
0
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3
replies
1.5k
views
goseq after edgeR
edger goseq
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 10
0
votes
2
replies
1.7k
views
GOseq: Correct for gene length or read count?
goseq dexseq
6.7 years ago • updated 6.6 years ago i.sudbery ▴ 30
1
vote
1
reply
2.8k
views
goseq: In pcls(G) : initial point very close to some inequality constraints
goseq warning message pwf mgcv
updated 6.7 years ago by ▴ 310 • written 6.7 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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