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KEGG
•
reset
0
votes
0
replies
115
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
11 days ago
cereyredondo
• 0
0
votes
3
replies
297
views
pathview error
KEGGgraph
KEGG
updated 9 weeks ago by
Guido Hooiveld
★ 4.0k • written 9 weeks ago by
Fara
• 0
0
votes
0
replies
130
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
10 weeks ago
danalvoronov
▴ 10
1
vote
1
reply
216
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 3 months ago by
James W. MacDonald
66k • written 3 months ago by
fernanda.backsouza
▴ 10
2
votes
13
replies
1.1k
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
3 months ago
fernanda.backsouza
▴ 10
3
votes
2
replies
335
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 3 months ago by
Guido Hooiveld
★ 4.0k • written 3 months ago by
fernanda.backsouza
▴ 10
2
votes
2
replies
379
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
3 months ago
julia_mcdonough
• 0
2
votes
2
replies
343
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 5 months ago by
Guido Hooiveld
★ 4.0k • written 5 months ago by
cinzia.spagnoli
• 0
0
votes
0
replies
439
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
9 months ago
mch
• 0
0
votes
3
replies
1.6k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 9 months ago by
Benji Bromberg
▴ 20 • written 10 months ago by
Mauricio Diego
• 0
3
votes
2
replies
1.3k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 11 months ago by
Guido Hooiveld
★ 4.0k • written 11 months ago by
Milan
▴ 10
0
votes
0
replies
421
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
12 months ago
georgii.vdovin
• 0
1
vote
4
replies
1.3k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
13 months ago
Jiyoung Lee
• 0
0
votes
1
reply
634
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 13 months ago by
Michael Love
42k • written 14 months ago by
Fred
• 0
0
votes
5
replies
1.5k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
15 months ago • updated 14 months ago
ruba-mahmoud
• 0
1
vote
3
replies
1.3k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 15 months ago by
Guido Hooiveld
★ 4.0k • written 15 months ago by
m-bihie
▴ 10
0
votes
13
replies
6.0k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
16 months ago
Laia
▴ 10
0
votes
5
replies
1.4k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 16 months ago by
andrewsm
• 0
4
votes
11
replies
3.0k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 14 months ago by
Aung
• 0 • written 16 months ago by
pedro-marra
▴ 10
4
votes
2
replies
5.0k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 17 months ago by
Erqiang Hu
▴ 50 • written 17 months ago by
redafazazi
• 0
1
vote
7
replies
2.2k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 17 months ago by
Basti
▴ 780 • written 17 months ago by
ruiqi.li
▴ 10
2
votes
6
replies
2.4k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 6 months ago by
Guido Hooiveld
★ 4.0k • written 17 months ago by
ruiqi.li
▴ 10
1
vote
3
replies
1.3k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 19 months ago by
James W. MacDonald
66k • written 20 months ago by
Arctic
• 0
4
votes
2
replies
2.4k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
21 months ago
Wuschel
▴ 10
0
votes
2
replies
774
views
Shivani
kegg
updated 21 months ago by
deeenes
▴ 50 • written 21 months ago by
Shivani
• 0
4
votes
6
replies
4.0k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 23 months ago by
Guido Hooiveld
★ 4.0k • written 2.1 years ago by
rama
▴ 10
3
votes
13
replies
2.8k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
23 months ago • updated 17 months ago
nute11a
▴ 10
0
votes
3
replies
1.0k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
24 months ago
abf
▴ 30
1
vote
1
reply
1.3k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG
UniProt.ws
updated 24 months ago by
James W. MacDonald
66k • written 24 months ago by
Recep
▴ 20
0
votes
2
replies
947
views
How do we get genes involved in all immune system pathways?
keggorthology
KEGG
updated 24 months ago by
sandmann.t
▴ 70 • written 2.0 years ago by
Recep
▴ 20
1
vote
3
replies
2.1k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 5 months ago by
cinzia.spagnoli
• 0 • written 2.1 years ago by
AP
• 0
0
votes
2
replies
3.5k
views
KEGG Pathway in R
keggrespathways
KEGG
updated 2.1 years ago by
Kevin Blighe
★ 4.0k • written 2.1 years ago by
salethlr
• 0
0
votes
1
reply
923
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
Aditya
• 0
0
votes
1
reply
1.3k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing
KEGG
GO
updated 2.5 years ago by
Kevin Blighe
★ 4.0k • written 2.5 years ago by
Omurice
• 0
0
votes
0
replies
877
views
Editing KEGG pathways in R
KEGG
2.7 years ago
Jordan
• 0
1
vote
0
replies
1.4k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
2.8 years ago
makrez
▴ 10
1
vote
0
replies
1.4k
views
documentation on clusterProfiler output
clusterProfiler
KEGG
2.8 years ago
rafaela.perez
▴ 10
0
votes
6
replies
4.0k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
3.0 years ago
Bogdan
▴ 670
0
votes
2
replies
2.0k
views
Drawing custom KEGG pathways
pathview
KEGG
3.2 years ago
curiousmind007
▴ 10
0
votes
2
replies
2.3k
views
Can't install KEGGprofile
KEGG
RNASeq
updated 3.2 years ago by
James W. MacDonald
66k • written 3.2 years ago by
Sophie
• 0
0
votes
0
replies
1.1k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
3.4 years ago
jol.espinoz
▴ 40
6
votes
5
replies
1.7k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.4 years ago by
Luo Weijun
★ 1.6k • written 3.4 years ago by
MOHAMMAD
• 0
2
votes
2
replies
1.2k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 3.6 years ago by
James W. MacDonald
66k • written 3.6 years ago by
ojong
• 0
0
votes
3
replies
1.2k
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 4.2 years ago by
James W. MacDonald
66k • written 4.2 years ago by
Bogdan
▴ 670
0
votes
1
reply
1.8k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
predeus
• 0
2
votes
2
replies
1.3k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db
KEGG
KEGGPATHNAME2ID
KEGGPATHID2EXTIT
updated 4.4 years ago by
James W. MacDonald
66k • written 4.4 years ago by
tobias-messmer
▴ 20
0
votes
0
replies
860
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
4.4 years ago
Assa Yeroslaviz
★ 1.5k
3
votes
1
reply
1.2k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG
R
offline
Pathway Enrichment
updated 4.4 years ago by
Gordon Smyth
51k • written 4.8 years ago by
omarrafiqued
▴ 50
6
votes
6
replies
5.3k
views
Finding enriched pathways from a gene list.
microarray
limma
kegg
ENTREZ
enrichment analysis
updated 4.4 years ago by
Gordon Smyth
51k • written 4.4 years ago by
omarrafiqued
▴ 50
0
votes
0
replies
972
views
gage function problem in R
gage
R
kegg
pathview
updated 4.5 years ago by
Michael Love
42k • written 4.5 years ago by
eozcan
• 0
50 results • Page
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Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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