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kegg
•
reset
1
vote
3
replies
2.4k
views
Regarding the issue of background genes in enrichment analysis
KEGG
goTools
seqTools
written 5 months ago by
17506483572
▴ 10
0
votes
4
replies
3.2k
views
Drawing custom KEGG pathways
pathview
KEGG
written 4.6 years ago by
curiousmind007
▴ 10
0
votes
1
reply
773
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler
KEGG
10 months ago
Jessica
• 0
0
votes
2
replies
947
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
10 months ago
ingrid.h
• 0
1
vote
4
replies
951
views
pathview - multiple states
pathview
Pathways
KEGG
12 months ago
Philippine
• 0
1
vote
2
replies
834
views
Student
metaboliteIDmapping
Metabolomics
KEGG
updated 15 months ago by
deeenes
▴ 60 • written 15 months ago by
vipinsapla
• 0
0
votes
0
replies
613
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
17 months ago
cereyredondo
• 0
0
votes
3
replies
1.2k
views
pathview error
KEGGgraph
KEGG
updated 19 months ago by
Guido Hooiveld
★ 4.1k • written 19 months ago by
Fara
• 0
0
votes
0
replies
521
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
19 months ago
danalvoronov
▴ 10
1
vote
1
reply
770
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 20 months ago by
James W. MacDonald
68k • written 20 months ago by
fernanda.backsouza
▴ 30
5
votes
13
replies
4.2k
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
20 months ago
fernanda.backsouza
▴ 30
4
votes
2
replies
963
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 20 months ago by
Guido Hooiveld
★ 4.1k • written 20 months ago by
fernanda.backsouza
▴ 30
2
votes
4
replies
2.4k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
written 20 months ago by
julia_mcdonough
• 0
2
votes
2
replies
787
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 22 months ago by
Guido Hooiveld
★ 4.1k • written 22 months ago by
cinzia.spagnoli
• 0
0
votes
0
replies
863
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
2.1 years ago
mch
• 0
0
votes
4
replies
4.0k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 14 months ago by
Evan
• 0 • written 2.3 years ago by
Mauricio Diego
• 0
3
votes
2
replies
2.9k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 2.4 years ago by
Guido Hooiveld
★ 4.1k • written 2.4 years ago by
Milan
▴ 10
0
votes
0
replies
836
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
2.4 years ago
georgii.vdovin
• 0
1
vote
4
replies
2.2k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
2.5 years ago
Jiyoung Lee
• 0
0
votes
1
reply
1.1k
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 2.6 years ago by
Michael Love
43k • written 2.6 years ago by
Fred
• 0
0
votes
5
replies
2.9k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
2.7 years ago • updated 2.6 years ago
ruba-mahmoud
• 0
1
vote
3
replies
2.4k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 2.7 years ago by
Guido Hooiveld
★ 4.1k • written 2.7 years ago by
m-bihie
▴ 10
0
votes
13
replies
14k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
2.8 years ago
Laia
▴ 10
0
votes
5
replies
2.3k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 2.8 years ago by
andrewsm
• 0
4
votes
11
replies
5.4k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 2.6 years ago by
Aung
• 0 • written 2.8 years ago by
pedro-marra
▴ 10
4
votes
2
replies
7.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 2.8 years ago by
Erqiang Hu
▴ 50 • written 2.8 years ago by
redafazazi
• 0
1
vote
7
replies
4.2k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 2.8 years ago by
Basti
▴ 780 • written 2.8 years ago by
ruiqi.li
▴ 10
2
votes
6
replies
5.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 23 months ago by
Guido Hooiveld
★ 4.1k • written 2.8 years ago by
ruiqi.li
▴ 10
1
vote
3
replies
2.1k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 3.0 years ago by
James W. MacDonald
68k • written 3.1 years ago by
Arctic
• 0
4
votes
2
replies
5.3k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
3.2 years ago
Wuschel
▴ 10
0
votes
2
replies
1.2k
views
Shivani
kegg
updated 3.2 years ago by
deeenes
▴ 60 • written 3.2 years ago by
Shivani
• 0
4
votes
6
replies
5.9k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 3.3 years ago by
Guido Hooiveld
★ 4.1k • written 3.5 years ago by
rama
▴ 10
3
votes
13
replies
4.3k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
3.3 years ago • updated 2.9 years ago
nute11a
▴ 10
0
votes
3
replies
1.7k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
3.4 years ago
abf
▴ 30
1
vote
1
reply
1.9k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG
UniProt.ws
updated 3.4 years ago by
James W. MacDonald
68k • written 3.4 years ago by
Recep
▴ 20
0
votes
2
replies
1.5k
views
How do we get genes involved in all immune system pathways?
keggorthology
KEGG
updated 3.4 years ago by
sandmann.t
▴ 70 • written 3.4 years ago by
Recep
▴ 20
1
vote
3
replies
3.2k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 22 months ago by
cinzia.spagnoli
• 0 • written 3.5 years ago by
AP
• 0
0
votes
2
replies
4.3k
views
KEGG Pathway in R
keggrespathways
KEGG
updated 3.6 years ago by
Kevin Blighe
★ 4.0k • written 3.6 years ago by
salethlr
• 0
0
votes
1
reply
1.4k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 3.7 years ago by
Michael Love
43k • written 3.7 years ago by
Aditya
• 0
0
votes
1
reply
2.0k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing
KEGG
GO
updated 3.9 years ago by
Kevin Blighe
★ 4.0k • written 3.9 years ago by
Omurice
• 0
0
votes
0
replies
1.3k
views
Editing KEGG pathways in R
KEGG
4.2 years ago
Jordan
• 0
1
vote
0
replies
2.2k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
4.2 years ago
makrez
▴ 10
1
vote
0
replies
2.0k
views
documentation on clusterProfiler output
clusterProfiler
KEGG
4.2 years ago
rafaela.perez
▴ 10
0
votes
6
replies
7.0k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
4.4 years ago
Bogdan
▴ 670
0
votes
2
replies
2.9k
views
Can't install KEGGprofile
KEGG
RNASeq
updated 4.6 years ago by
James W. MacDonald
68k • written 4.6 years ago by
Sophie
• 0
0
votes
0
replies
1.7k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
4.8 years ago
jol.espinoz
▴ 40
6
votes
5
replies
2.3k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 4.8 years ago by
Luo Weijun
★ 1.6k • written 4.8 years ago by
MOHAMMAD
• 0
2
votes
2
replies
1.7k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 5.0 years ago by
James W. MacDonald
68k • written 5.0 years ago by
ojong
• 0
0
votes
3
replies
1.7k
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
Bogdan
▴ 670
0
votes
1
reply
2.8k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
predeus
• 0
113 results • Page
1 of 3
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Answer: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink
by
ATpoint
★ 5.0k
> and I first used the normalized counts You would not use these normalized counts for PCA as they're not on log2 scale. As such, the feat…
Comment: EuroBioC2026 abstract submission is open!
by
TikTsokaasocissalpc
• 0
Submitting abstracts for EuroBioC2026 can be exciting but organizing ideas is key. A Random Word Generator [visit][1] can help create uniqu…
Comment: DESeq2 on non-RNASeq counts data
by
TikTsokaasocissalpc
• 0
In data analysis, behavior differences based on data type are common. Similarly, Best EDI Software adapts to non-standard transaction volum…
Comment: blockwiseModule crashes in the end and doesn't generate modules
by
gexose2839
• 0
Sounds good. @[time][1] [1]: https://timeduration.github.io
Comment: PFAM formats changed - is it still possible to use this with ISA?
by
TikTsokaasocissalpc
• 0
For mobile gaming enthusiasts, 3 Patti Lucky offers a seamless experience, unlike the frustration Harris faced with incompatible PFAM resul…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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