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KEGG
•
reset
1
vote
13
replies
350
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
8 days ago • updated 5 days ago
fernanda.backsouza
▴ 10
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
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
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 13 months ago by
andrewsm
• 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
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
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 10 weeks ago by
cinzia.spagnoli
• 0 • written 23 months ago by
AP
• 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
2
votes
2
replies
181
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
17 days ago
julia_mcdonough
• 0
3
votes
2
replies
190
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 7 days ago by
Guido Hooiveld
★ 3.9k • written 10 days ago by
fernanda.backsouza
▴ 10
2
votes
2
replies
244
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 10 weeks ago by
Guido Hooiveld
★ 3.9k • written 10 weeks ago by
cinzia.spagnoli
• 0
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
1
reply
1.5k
views
ClusterProfiler - enrichKEGG on specific pathways
kegg
enrichkegg
clusterprofiler
updated 5 months ago by
EvaLan
• 0 • written 5.8 years ago by
bekah
▴ 40
0
votes
1
reply
557
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 11 months ago by
Michael Love
41k • written 11 months ago by
Fred
• 0
1
vote
1
reply
90
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 6 days ago by
James W. MacDonald
65k • written 6 days ago by
fernanda.backsouza
▴ 10
0
votes
0
replies
346
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
9 months ago
georgii.vdovin
• 0
0
votes
0
replies
349
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
6 months ago
mch
• 0
18 results • Page
1 of 1
Recent ...
Replies
Comment: Assist me in determining whether the analysis process using the limma package ha
by
SSSJec
• 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score?
by
Gordon Smyth
50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
Chris
• 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
by
alserg
▴ 260
fgsea doesn't require the presence of deferentially expressed genes, it takes as the input the differential expression-based ranking of all…
Comment: Why p value inconsistent when using different number of pathway score?
by
Chris
• 0
Thanks Robert for an educative response!
Votes
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
Comment: Why p value inconsistent when using different number of pathway score?
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