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KEGG
•
reset
2
votes
13
replies
440
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
18 days ago • updated 15 days ago
fernanda.backsouza
▴ 10
1
vote
1
reply
121
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 16 days ago by
James W. MacDonald
65k • written 16 days ago by
fernanda.backsouza
▴ 10
3
votes
2
replies
220
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 17 days ago by
Guido Hooiveld
★ 3.9k • written 20 days ago by
fernanda.backsouza
▴ 10
2
votes
2
replies
203
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
27 days ago
julia_mcdonough
• 0
2
votes
2
replies
268
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 11 weeks ago by
Guido Hooiveld
★ 3.9k • written 11 weeks ago by
cinzia.spagnoli
• 0
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 11 weeks ago by
cinzia.spagnoli
• 0 • written 23 months ago by
AP
• 0
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 4 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 5 months ago by
EvaLan
• 0 • written 5.8 years ago by
bekah
▴ 40
0
votes
0
replies
360
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
6 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
1.2k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 7 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
355
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
9 months ago
georgii.vdovin
• 0
1
vote
4
replies
1.1k
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
565
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 11 months ago by
Michael Love
42k • written 11 months ago by
Fred
• 0
4
votes
11
replies
2.6k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 11 months ago by
Aung
• 0 • written 14 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 12 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
ruba-mahmoud
• 0
18 results • Page
1 of 1
Recent ...
Replies
Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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