Showing : KEGG • reset
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KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
19 days ago Jessica • 0
0
votes
2
replies
521
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
4 weeks ago • updated 17 days ago ingrid.h • 0
1
vote
4
replies
476
views
pathview - multiple states
pathview Pathways KEGG
12 weeks ago Philippine • 0
1
vote
2
replies
436
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 5 months ago by ▴ 60 • written 5 months ago by • 0
0
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0
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375
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
7 months ago cereyredondo • 0
0
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3
replies
829
views
pathview error
KEGGgraph KEGG
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
0
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0
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308
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
9 months ago danalvoronov ▴ 10
1
vote
1
reply
450
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 10 months ago by 68k • written 10 months ago by ▴ 30
5
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13
replies
2.7k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
10 months ago fernanda.backsouza ▴ 30
4
votes
2
replies
623
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 30
2
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3
replies
1.2k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 3 months ago by • 0 • written 10 months ago by • 0
2
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2
replies
560
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
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0
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631
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
16 months ago mch • 0
0
votes
4
replies
2.8k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 4 months ago by • 0 • written 17 months ago by • 0
3
votes
2
replies
2.2k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 18 months ago by ★ 4.1k • written 18 months ago by ▴ 10
0
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0
replies
591
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
19 months ago georgii.vdovin • 0
1
vote
4
replies
1.7k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
20 months ago Jiyoung Lee • 0
0
votes
1
reply
829
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 21 months ago by 43k • written 21 months ago by • 0
0
votes
5
replies
2.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
22 months ago ruba-mahmoud • 0
1
vote
3
replies
1.8k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 23 months ago by ★ 4.1k • written 23 months ago by ▴ 10
0
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13
replies
9.6k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
23 months ago Laia ▴ 10
0
votes
5
replies
1.9k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 23 months ago by • 0
4
votes
11
replies
4.2k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 21 months ago by • 0 • written 24 months ago by ▴ 10
4
votes
2
replies
6.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 2.0 years ago by ▴ 50 • written 2.0 years ago by • 0
1
vote
7
replies
3.1k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by ▴ 10
2
votes
6
replies
3.6k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 13 months ago by ★ 4.1k • written 2.0 years ago by ▴ 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 2.2 years ago by 68k • written 2.3 years ago by • 0
4
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2
replies
3.8k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
2.4 years ago Wuschel ▴ 10
0
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2
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962
views
Shivani
kegg
updated 2.4 years ago by ▴ 60 • written 2.4 years ago by • 0
4
votes
6
replies
4.9k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.5 years ago by ★ 4.1k • written 2.7 years ago by ▴ 10
3
votes
13
replies
3.4k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.5 years ago • updated 2.1 years ago nute11a ▴ 10
0
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3
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1.3k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.6 years ago abf ▴ 30
1
vote
1
reply
1.6k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 2.6 years ago by 68k • written 2.6 years ago by ▴ 20
0
votes
2
replies
1.2k
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 2.6 years ago by ▴ 70 • written 2.6 years ago by ▴ 20
1
vote
3
replies
2.6k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 12 months ago by • 0 • written 2.7 years ago by • 0
0
votes
2
replies
3.9k
views
KEGG Pathway in R
keggrespathways KEGG
updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by • 0
0
votes
1
reply
1.1k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.9 years ago by 43k • written 2.9 years ago by • 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 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
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0
replies
1.1k
views
Editing KEGG pathways in R
KEGG
3.3 years ago Jordan • 0
1
vote
0
replies
1.8k
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
3.4 years ago rafaela.perez ▴ 10
0
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6
replies
5.1k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.6 years ago Bogdan ▴ 670
0
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2
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2.5k
views
Drawing custom KEGG pathways
pathview KEGG
3.8 years ago curiousmind007 ▴ 10
0
votes
2
replies
2.6k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
0
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0
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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
1.9k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.0 years ago by ★ 1.6k • written 4.0 years ago by • 0
2
votes
2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.2 years ago by 68k • written 4.2 years ago by • 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 68k • written 4.8 years ago by ▴ 670
0
votes
1
reply
2.3k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
2
votes
2
replies
1.6k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 5.0 years ago by 68k • written 5.0 years ago by ▴ 20
50 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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