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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
772
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler
KEGG
10 months ago
Jessica
• 0
0
votes
2
replies
936
views
How to visualize these pathways using pathview
Salmo_salar
RNASeq
KEGG
pathview
10 months ago
ingrid.h
• 0
1
vote
4
replies
947
views
pathview - multiple states
pathview
Pathways
KEGG
12 months ago
Philippine
• 0
1
vote
2
replies
829
views
Student
metaboliteIDmapping
Metabolomics
KEGG
updated 15 months ago by
deeenes
▴ 60 • written 15 months ago by
vipinsapla
• 0
0
votes
0
replies
610
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
519
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
769
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
961
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
785
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
856
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
834
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 2.5 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
2.7 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
4.9k
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
4.2k
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
1.6k
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
4.2k
views
KEGG Pathway in R
keggrespathways
KEGG
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 3.5 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
4.1 years ago
Jordan
• 0
1
vote
0
replies
2.1k
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
6.9k
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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Replies
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
I refered you to the DiffVar package 11 months ago. Did you consider it? Your clarification makes it clear that your issue is not with lim…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reply Gordon. I am also working on the project and have been tasked to reformulate and add some details. We're interested i…
Answer: How does contrasts.fit do in limma to extract comparisons with a model having in
by
Gordon Smyth
53k
The limma Users Guide explains how to test for interactions or to test for contrasts very easily. limma can work with any design matrix, bu…
Answer: NUPOP usage
by
shepherl
4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker?
by
fnfgame
• 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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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