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KEGG
•
reset
2
votes
2
replies
135
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
5 days ago
julia_mcdonough
• 0
2
votes
2
replies
229
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 8 weeks ago by
Guido Hooiveld
★ 3.9k • written 8 weeks ago by
cinzia.spagnoli
• 0
0
votes
0
replies
334
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
5 months ago
mch
• 0
0
votes
3
replies
1.1k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 6 months ago by
Benji Bromberg
▴ 20 • written 7 months ago by
Mauricio Diego
• 0
3
votes
2
replies
1.0k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 8 months ago by
Guido Hooiveld
★ 3.9k • written 8 months ago by
Milan
▴ 10
0
votes
0
replies
335
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
9 months ago
georgii.vdovin
• 0
1
vote
4
replies
1.0k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
10 months ago
Jiyoung Lee
• 0
0
votes
1
reply
545
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 10 months ago by
Michael Love
41k • written 10 months ago by
Fred
• 0
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
12 months ago • updated 11 months ago
ruba-mahmoud
• 0
1
vote
3
replies
1.1k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 12 months ago by
Guido Hooiveld
★ 3.9k • written 12 months ago by
m-bihie
▴ 10
0
votes
13
replies
4.5k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
13 months ago
Laia
▴ 10
0
votes
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 13 months ago by
andrewsm
• 0
4
votes
11
replies
2.4k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 11 months ago by
Aung
• 0 • written 13 months ago by
pedro-marra
▴ 10
4
votes
2
replies
4.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 13 months ago by
Erqiang Hu
▴ 50 • written 13 months ago by
redafazazi
• 0
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 13 months ago by
Basti
▴ 760 • written 13 months ago by
ruiqi.li
• 0
2
votes
6
replies
1.9k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 3 months ago by
Guido Hooiveld
★ 3.9k • written 13 months ago by
ruiqi.li
• 0
1
vote
3
replies
1.1k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 16 months ago by
James W. MacDonald
65k • written 16 months ago by
Arctic
• 0
4
votes
2
replies
1.8k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
18 months ago
Wuschel
▴ 10
0
votes
2
replies
656
views
Shivani
kegg
updated 18 months ago by
deeenes
▴ 30 • written 18 months ago by
Shivani
• 0
4
votes
6
replies
3.6k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 19 months ago by
Guido Hooiveld
★ 3.9k • written 22 months ago by
rama
▴ 10
3
votes
13
replies
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
20 months ago • updated 14 months ago
nute11a
▴ 10
0
votes
3
replies
933
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
20 months ago
abf
▴ 30
1
vote
1
reply
1.2k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG
UniProt.ws
updated 20 months ago by
James W. MacDonald
65k • written 20 months ago by
Recep
▴ 20
0
votes
2
replies
836
views
How do we get genes involved in all immune system pathways?
keggorthology
KEGG
updated 20 months ago by
sandmann.t
▴ 70 • written 21 months ago by
Recep
▴ 20
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 8 weeks ago by
cinzia.spagnoli
• 0 • written 22 months ago by
AP
• 0
0
votes
2
replies
3.3k
views
KEGG Pathway in R
keggrespathways
KEGG
updated 22 months ago by
Kevin Blighe
★ 3.9k • written 22 months ago by
salethlr
• 0
0
votes
1
reply
800
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 2.0 years ago by
Michael Love
41k • written 2.0 years ago by
Aditya
• 0
0
votes
1
reply
1.2k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing
KEGG
GO
updated 2.2 years ago by
Kevin Blighe
★ 3.9k • written 2.2 years ago by
Omurice
• 0
0
votes
0
replies
790
views
Editing KEGG pathways in R
KEGG
2.5 years ago
Jordan
• 0
1
vote
0
replies
1.3k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
2.5 years ago
makrez
▴ 10
1
vote
0
replies
1.2k
views
documentation on clusterProfiler output
clusterProfiler
KEGG
2.5 years ago
rafaela.perez
▴ 10
0
votes
6
replies
3.6k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
2.7 years ago
Bogdan
▴ 670
0
votes
2
replies
1.8k
views
Drawing custom KEGG pathways
pathview
KEGG
2.9 years ago
curiousmind007
▴ 10
0
votes
2
replies
2.1k
views
Can't install KEGGprofile
KEGG
RNASeq
updated 2.9 years ago by
James W. MacDonald
65k • written 2.9 years ago by
Sophie
• 0
0
votes
0
replies
975
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
3.1 years ago
jol.espinoz
▴ 40
6
votes
5
replies
1.5k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.1 years ago by
Luo Weijun
★ 1.6k • written 3.1 years ago by
MOHAMMAD
• 0
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
3
replies
1.1k
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
Bogdan
▴ 670
0
votes
1
reply
1.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 4.0 years ago by
Martin Morgan
25k • written 4.0 years ago by
predeus
• 0
2
votes
2
replies
1.2k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db
KEGG
KEGGPATHNAME2ID
KEGGPATHID2EXTIT
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
tobias-messmer
▴ 10
0
votes
0
replies
763
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
4.1 years ago
Assa Yeroslaviz
★ 1.5k
3
votes
1
reply
1.1k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG
R
offline
Pathway Enrichment
updated 4.2 years ago by
Gordon Smyth
50k • written 4.6 years ago by
omarrafiqued
▴ 50
6
votes
6
replies
5.0k
views
Finding enriched pathways from a gene list.
microarray
limma
kegg
ENTREZ
enrichment analysis
updated 4.2 years ago by
Gordon Smyth
50k • written 4.2 years ago by
omarrafiqued
▴ 50
0
votes
0
replies
863
views
gage function problem in R
gage
R
kegg
pathview
updated 4.2 years ago by
Michael Love
41k • written 4.2 years ago by
eozcan
• 0
4
votes
4
replies
1.7k
views
How I interpret this plot from pathview
pathview
kegg
r
pathway
4.4 years ago
AZ
▴ 30
0
votes
2
replies
884
views
how can I find a pathway
kegg
KEGGREST
4.4 years ago
Bioinformatics
▴ 30
0
votes
0
replies
941
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage
pathview
KEGG
Gene enrichment analysis
4.5 years ago
MimR
• 0
0
votes
0
replies
808
views
pvaluecutoff meaning in enrichKEGG
KEGG
RNAseq
4.6 years ago
sportiellomike
• 0
0
votes
0
replies
961
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview
Gene Mapping
KEGG
4.6 years ago
omarrafiqued
▴ 50
0
votes
2
replies
1.1k
views
Issue with xml files downloaded with `pathview()`
pathview
kegg
xml
updated 4.7 years ago by
Luo Weijun
★ 1.6k • written 4.8 years ago by
anamaria
▴ 10
50 results • Page
1 of 1
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Replies
Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark
by
jacques.imbert
• 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
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…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
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.
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