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KEGG
•
reset
0
votes
1
reply
228
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler
KEGG
7 weeks ago
Jessica
• 0
0
votes
2
replies
564
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
9 weeks ago • updated 7 weeks ago
ingrid.h
• 0
1
vote
4
replies
553
views
pathview - multiple states
pathview
Pathways
KEGG
4 months ago
Philippine
• 0
1
vote
2
replies
490
views
Student
metaboliteIDmapping
Metabolomics
KEGG
updated 6 months ago by
deeenes
▴ 60 • written 6 months ago by
vipinsapla
• 0
0
votes
0
replies
392
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
8 months ago
cereyredondo
• 0
0
votes
3
replies
909
views
pathview error
KEGGgraph
KEGG
updated 10 months ago by
Guido Hooiveld
★ 4.1k • written 10 months ago by
Fara
• 0
0
votes
0
replies
332
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
10 months ago
danalvoronov
▴ 10
1
vote
1
reply
475
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 11 months ago by
James W. MacDonald
68k • written 11 months ago by
fernanda.backsouza
▴ 30
5
votes
13
replies
3.0k
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
11 months ago
fernanda.backsouza
▴ 30
4
votes
2
replies
657
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 11 months ago by
Guido Hooiveld
★ 4.1k • written 11 months ago by
fernanda.backsouza
▴ 30
2
votes
4
replies
1.6k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
written 11 months ago by
julia_mcdonough
• 0
2
votes
2
replies
582
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 13 months ago by
Guido Hooiveld
★ 4.1k • written 13 months ago by
cinzia.spagnoli
• 0
0
votes
0
replies
656
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
17 months ago
mch
• 0
0
votes
4
replies
3.0k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 5 months ago by
Evan
• 0 • written 18 months ago by
Mauricio Diego
• 0
3
votes
2
replies
2.3k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 19 months ago by
Guido Hooiveld
★ 4.1k • written 19 months ago by
Milan
▴ 10
0
votes
0
replies
610
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
20 months ago
georgii.vdovin
• 0
1
vote
4
replies
1.8k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
21 months ago
Jiyoung Lee
• 0
0
votes
1
reply
851
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 22 months ago by
Michael Love
43k • written 22 months ago by
Fred
• 0
0
votes
5
replies
2.4k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
23 months ago
ruba-mahmoud
• 0
1
vote
3
replies
1.9k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 24 months ago by
Guido Hooiveld
★ 4.1k • written 2.0 years ago by
m-bihie
▴ 10
0
votes
13
replies
11k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
2.0 years ago
Laia
▴ 10
0
votes
5
replies
2.0k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 2.0 years ago by
andrewsm
• 0
4
votes
11
replies
4.5k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 22 months ago by
Aung
• 0 • written 2.1 years ago by
pedro-marra
▴ 10
4
votes
2
replies
6.5k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 2.1 years ago by
Erqiang Hu
▴ 50 • written 2.1 years ago by
redafazazi
• 0
1
vote
7
replies
3.3k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
ruiqi.li
▴ 10
2
votes
6
replies
3.8k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 15 months ago by
Guido Hooiveld
★ 4.1k • written 2.1 years ago by
ruiqi.li
▴ 10
1
vote
3
replies
1.7k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 2.3 years ago by
James W. MacDonald
68k • written 2.4 years ago by
Arctic
• 0
4
votes
2
replies
4.1k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
2.4 years ago
Wuschel
▴ 10
0
votes
2
replies
990
views
Shivani
kegg
updated 2.5 years ago by
deeenes
▴ 60 • written 2.5 years ago by
Shivani
• 0
4
votes
6
replies
5.1k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 2.6 years ago by
Guido Hooiveld
★ 4.1k • written 2.8 years ago by
rama
▴ 10
3
votes
13
replies
3.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
2.6 years ago • updated 2.2 years ago
nute11a
▴ 10
0
votes
3
replies
1.3k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
2.7 years ago
abf
▴ 30
1
vote
1
reply
1.7k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG
UniProt.ws
updated 2.7 years ago by
James W. MacDonald
68k • written 2.7 years ago by
Recep
▴ 20
0
votes
2
replies
1.2k
views
How do we get genes involved in all immune system pathways?
keggorthology
KEGG
updated 2.7 years ago by
sandmann.t
▴ 70 • written 2.7 years ago by
Recep
▴ 20
1
vote
3
replies
2.7k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 13 months ago by
cinzia.spagnoli
• 0 • written 2.8 years ago by
AP
• 0
0
votes
2
replies
3.9k
views
KEGG Pathway in R
keggrespathways
KEGG
updated 2.8 years ago by
Kevin Blighe
★ 4.0k • written 2.8 years ago by
salethlr
• 0
0
votes
1
reply
1.2k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 3.0 years ago by
Michael Love
43k • written 3.0 years ago by
Aditya
• 0
0
votes
1
reply
1.7k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing
KEGG
GO
updated 3.2 years ago by
Kevin Blighe
★ 4.0k • written 3.2 years ago by
Omurice
• 0
0
votes
0
replies
1.1k
views
Editing KEGG pathways in R
KEGG
3.4 years ago
Jordan
• 0
1
vote
0
replies
1.9k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
3.4 years ago
makrez
▴ 10
1
vote
0
replies
1.7k
views
documentation on clusterProfiler output
clusterProfiler
KEGG
3.5 years ago
rafaela.perez
▴ 10
0
votes
6
replies
5.4k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
3.7 years ago
Bogdan
▴ 670
0
votes
3
replies
2.7k
views
Drawing custom KEGG pathways
pathview
KEGG
written 3.9 years ago by
curiousmind007
▴ 10
0
votes
2
replies
2.7k
views
Can't install KEGGprofile
KEGG
RNASeq
updated 3.9 years ago by
James W. MacDonald
68k • written 3.9 years ago by
Sophie
• 0
0
votes
0
replies
1.3k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG
KEGGREST
keggorthology
Metagenomics
4.0 years ago
jol.espinoz
▴ 40
6
votes
5
replies
2.0k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 4.1 years ago by
Luo Weijun
★ 1.6k • written 4.1 years ago by
MOHAMMAD
• 0
2
votes
2
replies
1.5k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 4.3 years ago by
James W. MacDonald
68k • written 4.3 years ago by
ojong
• 0
0
votes
3
replies
1.4k
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 4.8 years ago by
James W. MacDonald
68k • written 4.8 years ago by
Bogdan
▴ 670
0
votes
1
reply
2.4k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 5.0 years ago by
Martin Morgan
25k • written 5.0 years ago by
predeus
• 0
2
votes
2
replies
1.7k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db
KEGG
KEGGPATHNAME2ID
KEGGPATHID2EXTIT
updated 5.0 years ago by
James W. MacDonald
68k • written 5.0 years ago by
tobias-messmer
▴ 20
50 results • Page
1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting
by
bd2000
▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
James W. MacDonald
68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin
by
ATpoint
★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt
by
darylruiz6545
• 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash
by
Alex
• 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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