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goseq
•
reset
1
vote
2
replies
229
views
supportedOrganisms() in goseq producing Error in names(trackIds)
goseq
Bioconductor
rtracklayer
5 weeks ago
thomas
• 0
1
vote
4
replies
402
views
goseq, warning and strange plot from nullp
goseq
11 weeks ago • updated 10 weeks ago
boczniak767
▴ 720
0
votes
1
reply
581
views
Downstream analysis with Differentially Expressed Genes
DESeq2
GO
goseq
FunctionalAnnotation
updated 17 months ago by
Laia
▴ 10 • written 17 months ago by
acram
• 0
0
votes
5
replies
1.9k
views
GO enrichment with non-model organism, supplying GO mappings
clusterProfiler
goseq
topGO
DESeq2
updated 22 months ago by
James W. MacDonald
65k • written 22 months ago by
Lucía
▴ 10
0
votes
2
replies
822
views
goseq: Wallenius Vs Fisher's Noncentral Hypergeometric Distribution
goseq
24 months ago • updated 23 months ago
Steve Pederson
▴ 170
0
votes
0
replies
736
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage
plot
RNASeq
goseq
updated 2.1 years ago by
Michael Love
41k • written 2.1 years ago by
m.glymenaki
• 0
1
vote
2
replies
801
views
Pathway analysis of RNAseq data using goseq package
Pathways
goseq
RNASeqData
2.1 years ago
m.glymenaki
• 0
1
vote
10
replies
2.4k
views
How to run Goseq for list of ensembl gene IDs
goseq
3.1 years ago • updated 3.0 years ago
Lucky
• 0
1
vote
4
replies
1.4k
views
goseq package loading issues
DESeq2
goseq
3.1 years ago
avinashi
• 0
3
votes
9
replies
1.9k
views
Warning message when performing Gene Ontology analysis with goseq using hg38
goseq
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
Nikolay Ivanov
• 0
2
votes
3
replies
1.6k
views
Gene Ontology Analysis of DE Genes
clusterProfiler
AnnotationDbi
OrgDb
goseq
updated 3.2 years ago by
James W. MacDonald
65k • written 3.2 years ago by
vanbelj
▴ 30
2
votes
2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 3.4 years ago by
James W. MacDonald
65k • written 3.4 years ago by
ojong
• 0
0
votes
1
reply
888
views
non-native GO annotation cannot be successfully introduced into Goseq
goseq
rnaseq
r
updated 3.5 years ago by
James W. MacDonald
65k • written 3.5 years ago by
citronxu
• 0
0
votes
0
replies
467
views
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
votes
2
replies
700
views
Goseq_analysis related help
goseq
3.8 years ago
kumararya563
• 0
1
vote
2
replies
879
views
GOSeq analysis in rice
goseq
3.8 years ago • updated 3.7 years ago
Jitendra
▴ 10
3
votes
2
replies
1.1k
views
Goseq analysis related help.
annotation
goseq
updated 3.8 years ago by
Steve Lianoglou
★ 13k • written 3.8 years ago by
kumararya563
• 0
0
votes
0
replies
819
views
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
votes
5
replies
1.7k
views
Downgrading R to 3.6.0 version (GOseq problem)
goseq
installation
4.3 years ago
gdalsky
▴ 40
0
votes
1
reply
2.1k
views
GO enrichment analysis graphs after goseq: any easy solutions?
go enrichment
gene ontology
goseq
go
4.6 years ago
Raito92
▴ 60
2
votes
6
replies
1.1k
views
Can't install GOSEQ (dependency problem) on CentOS 7!
goseq
r package
r
updated 4.6 years ago by
Mike Smith
★ 6.5k • written 4.6 years ago by
Raito92
▴ 60
1
vote
1
reply
1.3k
views
GOseq analysis with only upregulated or downregulated genes
goseq
updated 5.0 years ago by
Nadia Davidson
▴ 310 • written 5.0 years ago by
charles.foster
▴ 160
2
votes
2
replies
1.0k
views
Using GOseq for custom gene set enrichment test
goseq
updated 5.2 years ago by
Gordon Smyth
50k • written 5.2 years ago by
kubovcij
• 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
James W. MacDonald
65k • written 5.4 years ago by
mico
• 0
1
vote
3
replies
1.8k
views
goseq: Formatting category list for use with goseq
goseq
category test
updated 5.6 years ago by
James W. MacDonald
65k • written 5.6 years ago by
Mthabisi Moyo
▴ 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
Gordon Smyth
50k • written 5.7 years ago by
Juan
• 0
3
votes
2
replies
999
views
numInCat in goseq inconsistent with value obtained from org.Hs.eg.db
goseq
updated 5.7 years ago by
James W. MacDonald
65k • written 5.7 years ago by
siajunren
• 0
1
vote
9
replies
2.1k
views
Using goseq with unsupported organism
goseq
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
Mehdi
• 0
0
votes
0
replies
924
views
GOseq No Underrepresented Categories
goseq
go enrichment
5.8 years ago
mart1139
• 0
8
votes
10
replies
1.6k
views
Genes listed in GO categories
goseq
biomart
updated 5.8 years ago by
Gordon Smyth
50k • written 5.9 years ago by
frezende
• 0
0
votes
2
replies
865
views
goseq with hypergeometric method
goseq
updated 5.9 years ago by
Gordon Smyth
50k • written 5.9 years ago by
sharvari gujja
▴ 40
0
votes
0
replies
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
votes
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
replies
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
votes
2
replies
3.6k
views
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
Michael Love
41k • written 6.2 years ago by
josef.oeckl
• 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
Gordon Smyth
50k • written 6.2 years ago by
joelrosa
• 0
0
votes
1
reply
2.6k
views
installation of package 'goseq' had non-zero exit status
goseq
installation
updated 6.4 years ago by
Martin Morgan
25k • written 6.4 years ago by
philipp.voss
• 0
0
votes
1
reply
1.6k
views
PANTHER.db- external pointer error
goseq
pantherdb
pathway analysis
gene ontology
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 years ago by
krc3004
▴ 10
1
vote
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
James W. MacDonald
65k • written 6.5 years ago by
JMallory
• 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
Gordon Smyth
50k • written 6.5 years ago by
pereyra.s
• 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
Martin Morgan
25k • written 6.6 years ago by
veerle
• 0
0
votes
2
replies
1.6k
views
bias.data vector must have the same length as DEgenes vector!
edger
goseq
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
mictadlo
▴ 10
0
votes
0
replies
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
Michael Lawrence
★ 11k • written 6.6 years ago by
mictadlo
▴ 10
0
votes
3
replies
1.5k
views
goseq after edgeR
edger
goseq
updated 6.6 years ago by
Aaron Lun
★ 28k • written 6.6 years ago by
mictadlo
▴ 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
Nadia Davidson
▴ 310 • written 6.7 years ago by
heikki.sarin
▴ 10
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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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