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Showing :
Kegg
•
reset
1
vote
13
replies
275
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
4 days ago • updated 1 day ago
fernanda.backsouza
▴ 10
1
vote
1
reply
62
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 2 days ago by
James W. MacDonald
65k • written 2 days ago by
fernanda.backsouza
▴ 10
3
votes
2
replies
164
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 3 days ago by
Guido Hooiveld
★ 3.9k • written 6 days ago by
fernanda.backsouza
▴ 10
2
votes
2
replies
168
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
13 days ago
julia_mcdonough
• 0
2
votes
2
replies
235
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 9 weeks ago by
Guido Hooiveld
★ 3.9k • written 9 weeks ago by
cinzia.spagnoli
• 0
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 9 weeks ago by
cinzia.spagnoli
• 0 • written 22 months ago by
AP
• 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 14 months ago by
ruiqi.li
▴ 10
0
votes
1
reply
1.5k
views
ClusterProfiler - enrichKEGG on specific pathways
kegg
enrichkegg
clusterprofiler
updated 4 months ago by
EvaLan
• 0 • written 5.7 years ago by
bekah
▴ 40
0
votes
0
replies
344
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
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 13 months ago by
andrewsm
• 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
1.1k
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
344
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
556
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 10 months ago by
Michael Love
41k • written 11 months ago by
Fred
• 0
4
votes
11
replies
2.5k
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
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG
GAGE
NaN
R
DESeq2
updated 11 months ago by
Rob
• 0 • written 5.5 years ago by
owen.donohoe
• 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
4.6k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
13 months ago
Laia
▴ 10
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 13 months ago by
Basti
▴ 780 • written 14 months ago by
ruiqi.li
▴ 10
4
votes
2
replies
4.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 14 months ago by
Erqiang Hu
▴ 50 • written 14 months ago by
redafazazi
• 0
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
1
vote
3
replies
1.2k
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 17 months ago by
Arctic
• 0
4
votes
2
replies
1.9k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
18 months ago
Wuschel
▴ 10
0
votes
2
replies
665
views
Shivani
kegg
updated 18 months ago by
deeenes
▴ 40 • 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 20 months ago by
Guido Hooiveld
★ 3.9k • written 22 months ago by
rama
▴ 10
0
votes
3
replies
943
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 21 months ago by
James W. MacDonald
65k • written 21 months ago by
Recep
▴ 20
0
votes
2
replies
846
views
How do we get genes involved in all immune system pathways?
keggorthology
KEGG
updated 21 months ago by
sandmann.t
▴ 70 • written 21 months ago by
Recep
▴ 20
0
votes
2
replies
3.3k
views
KEGG Pathway in R
keggrespathways
KEGG
updated 23 months ago by
Kevin Blighe
★ 3.9k • written 23 months ago by
salethlr
• 0
0
votes
1
reply
820
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 2.1 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
803
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
2.6 years ago
rafaela.perez
▴ 10
0
votes
6
replies
3.7k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
2.7 years ago
Bogdan
▴ 670
2
votes
3
replies
4.8k
views
Pathview None of the genes or compounds mapped to the pathway
pathview
pathways
KEGG
empty map
updated 2.8 years ago by
najib
• 0 • written 8.3 years ago by
Dani
▴ 20
1
vote
5
replies
2.9k
views
KEGG enrichment for non-model
kegg
pathway analysis
non-model
gage
pathview
updated 2.8 years ago by
najib
• 0 • written 5.8 years ago by
bekah
▴ 40
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
989
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
772
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
4.1 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 4.2 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
50 results • Page
1 of 1
Recent ...
Replies
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh snap. Foiled again. Here it is with spaces & ge ; and & lt ;
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Oh LOL. My markdown got edited by the markdown editor! What is between the p and 50 in the first case is the HTML for greater than or equal…
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
Ah, good point. You could instead try ``` > library(ggtext) > keyvals.shape = c(rep(3,10), rep(2,8)) > names(keyvals.shape) = ifelse(keyva…
Votes
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
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