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Showing :
kegg
•
reset
1
vote
4
replies
311
views
pathview - multiple states
pathview
Pathways
KEGG
17 days ago • updated 16 days ago
Philippine
• 0
1
vote
2
replies
333
views
Student
metaboliteIDmapping
Metabolomics
KEGG
updated 3 months ago by
deeenes
▴ 60 • written 3 months ago by
vipinsapla
• 0
0
votes
0
replies
315
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
5 months ago
cereyredondo
• 0
0
votes
3
replies
637
views
pathview error
KEGGgraph
KEGG
updated 7 months ago by
Guido Hooiveld
★ 4.1k • written 7 months ago by
Fara
• 0
0
votes
0
replies
250
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
7 months ago
danalvoronov
▴ 10
1
vote
1
reply
379
views
Cannabis OrgDb
KEGGgraph
org.Cs.eg.db
clusterProfiler
KEGG
AnnotationHubSoftware
updated 8 months ago by
James W. MacDonald
67k • written 8 months ago by
fernanda.backsouza
▴ 30
5
votes
13
replies
2.2k
views
Trying to use enrichGO
clusterProfiler
GenomicDistributionsData
KEGG
8 months ago
fernanda.backsouza
▴ 30
4
votes
2
replies
535
views
Cannabis and KEGGgraph
KEGGREST
GenomicDistributionsData
KEGGgraph
KEGG
updated 8 months ago by
Guido Hooiveld
★ 4.1k • written 8 months ago by
fernanda.backsouza
▴ 30
2
votes
3
replies
906
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways
clusterProfiler
gseKEGG
KEGG
updated 5 weeks ago by
josephasmith1310
• 0 • written 8 months ago by
julia_mcdonough
• 0
2
votes
2
replies
496
views
Error in enrichKEGG for a model organism
enrichKEGG
KEGGgraph
KEGG
updated 10 months ago by
Guido Hooiveld
★ 4.1k • written 10 months ago by
cinzia.spagnoli
• 0
0
votes
0
replies
572
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST
KEGG
RNASeq
13 months ago
mch
• 0
0
votes
4
replies
2.5k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 10 weeks ago by
Evan
• 0 • written 15 months ago by
Mauricio Diego
• 0
3
votes
2
replies
1.9k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG
DESeq2
biomaRt
clusterProfiler
org.Mm.eg.db
updated 16 months ago by
Guido Hooiveld
★ 4.1k • written 16 months ago by
Milan
▴ 10
0
votes
0
replies
534
views
Downstream analysis of DEG for non-model organisms.
axolotl
KEGG
GOstats
clusterProfiler
17 months ago
georgii.vdovin
• 0
1
vote
4
replies
1.6k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
18 months ago
Jiyoung Lee
• 0
0
votes
1
reply
759
views
DESeq2 + analysis question for design with uneven time point design
timecourse
KEGG
DESeq2
updated 18 months ago by
Michael Love
43k • written 19 months ago by
Fred
• 0
0
votes
5
replies
2.0k
views
enrichKEGG function error
cluster
clusterProfiler
KEGG
20 months ago • updated 19 months ago
ruba-mahmoud
• 0
1
vote
3
replies
1.7k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG
clusterProfiler
Bioconductor
updated 20 months ago by
Guido Hooiveld
★ 4.1k • written 20 months ago by
m-bihie
▴ 10
0
votes
13
replies
8.1k
views
KEGG enrichment in R and gene IDs
KEGG
enrichKEGG
R
entrezid
21 months ago
Laia
▴ 10
0
votes
5
replies
1.7k
views
[limma::kegga] Pathway names all NA
KEGG
limma
written 21 months ago by
andrewsm
• 0
4
votes
11
replies
3.8k
views
Sudden error with KEGG analysis using gometh
KEGG
gometh
updated 19 months ago by
Aung
• 0 • written 21 months ago by
pedro-marra
▴ 10
4
votes
2
replies
5.8k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG
clusterProfiler
updated 21 months ago by
Erqiang Hu
▴ 50 • written 21 months ago by
redafazazi
• 0
1
vote
7
replies
2.7k
views
Problem with universe argument in enrichKEGG
KEGG
clusterProfiler
keggorthology
updated 21 months ago by
Basti
▴ 780 • written 22 months ago by
ruiqi.li
▴ 10
2
votes
6
replies
3.1k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG
clusterProfiler
updated 11 months ago by
Guido Hooiveld
★ 4.1k • written 22 months ago by
ruiqi.li
▴ 10
1
vote
3
replies
1.6k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 24 months ago by
James W. MacDonald
67k • written 2.1 years ago by
Arctic
• 0
4
votes
2
replies
3.4k
views
Is there any description available for KEGG Pathway Edge Types
KEGG
SystemsBiology
KEGGgraph
ontology
2.2 years ago
Wuschel
▴ 10
0
votes
2
replies
907
views
Shivani
kegg
updated 2.2 years ago by
deeenes
▴ 60 • written 2.2 years ago by
Shivani
• 0
4
votes
6
replies
4.6k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 2.3 years ago by
Guido Hooiveld
★ 4.1k • written 2.5 years ago by
rama
▴ 10
3
votes
13
replies
3.1k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
2.3 years ago • updated 22 months ago
nute11a
▴ 10
0
votes
3
replies
1.2k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST
ROntoTools
KEGG
KEGGgraph
2.4 years ago
abf
▴ 30
1
vote
1
reply
1.5k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG
UniProt.ws
updated 2.4 years ago by
James W. MacDonald
67k • written 2.4 years ago by
Recep
▴ 20
0
votes
2
replies
1.1k
views
How do we get genes involved in all immune system pathways?
keggorthology
KEGG
updated 2.4 years ago by
sandmann.t
▴ 70 • written 2.4 years ago by
Recep
▴ 20
1
vote
3
replies
2.5k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 10 months ago by
cinzia.spagnoli
• 0 • written 2.5 years ago by
AP
• 0
0
votes
2
replies
3.8k
views
KEGG Pathway in R
keggrespathways
KEGG
updated 2.6 years ago by
Kevin Blighe
★ 4.0k • written 2.6 years ago by
salethlr
• 0
0
votes
1
reply
1.0k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics
DESeq2
metagenomeSeq
edgeR
KEGG
updated 2.7 years ago by
Michael Love
43k • written 2.7 years ago by
Aditya
• 0
0
votes
1
reply
1.5k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing
KEGG
GO
updated 2.9 years ago by
Kevin Blighe
★ 4.0k • written 2.9 years ago by
Omurice
• 0
0
votes
0
replies
999
views
Editing KEGG pathways in R
KEGG
3.1 years ago
Jordan
• 0
1
vote
0
replies
1.7k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
3.2 years ago
makrez
▴ 10
1
vote
0
replies
1.5k
views
documentation on clusterProfiler output
clusterProfiler
KEGG
3.2 years ago
rafaela.perez
▴ 10
0
votes
6
replies
4.5k
views
extracting the KEGG pathway for a set of genes
Pathways
KEGG
3.4 years ago
Bogdan
▴ 670
0
votes
2
replies
2.3k
views
Drawing custom KEGG pathways
pathview
KEGG
3.6 years ago
curiousmind007
▴ 10
0
votes
2
replies
2.5k
views
Can't install KEGGprofile
KEGG
RNASeq
updated 3.6 years ago by
James W. MacDonald
67k • written 3.6 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
3.8 years ago
jol.espinoz
▴ 40
6
votes
5
replies
1.8k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.8 years ago by
Luo Weijun
★ 1.6k • written 3.8 years ago by
MOHAMMAD
• 0
2
votes
2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG
Pathways
GO
goseq
updated 4.0 years ago by
James W. MacDonald
67k • written 4.0 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 4.6 years ago by
James W. MacDonald
67k • written 4.6 years ago by
Bogdan
▴ 670
0
votes
1
reply
2.1k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest
software error
pathways
modules
kegg
updated 4.7 years ago by
Martin Morgan
25k • written 4.7 years ago by
predeus
• 0
2
votes
2
replies
1.5k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db
KEGG
KEGGPATHNAME2ID
KEGGPATHID2EXTIT
updated 4.8 years ago by
James W. MacDonald
67k • written 4.8 years ago by
tobias-messmer
▴ 20
0
votes
0
replies
975
views
plotting Signalling Pathways using SPIA
SPIA
functional-analysis
Pathways
KEGG
4.8 years ago
Assa Yeroslaviz
★ 1.5k
3
votes
1
reply
1.4k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG
R
offline
Pathway Enrichment
updated 4.8 years ago by
Gordon Smyth
52k • written 5.2 years ago by
omarrafiqued
▴ 50
50 results • Page
1 of 1
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Replies
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
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43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
by
xiaofeiwang198266
• 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
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