Showing : KEGG • reset
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Regarding the issue of background genes in enrichment analysis
KEGG goTools seqTools
written 9 weeks ago by ▴ 10
0
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4
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3.1k
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Drawing custom KEGG pathways
pathview KEGG
written 4.3 years ago by ▴ 10
0
votes
1
reply
681
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
7 months ago Jessica • 0
0
votes
2
replies
778
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
7 months ago • updated 6 months ago ingrid.h • 0
1
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4
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784
views
pathview - multiple states
pathview Pathways KEGG
9 months ago Philippine • 0
1
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2
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725
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 11 months ago by ▴ 60 • written 11 months ago by • 0
0
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0
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509
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
14 months ago cereyredondo • 0
0
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3
replies
1.1k
views
pathview error
KEGGgraph KEGG
updated 15 months ago by ★ 4.1k • written 15 months ago by • 0
0
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0
replies
437
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
16 months ago danalvoronov ▴ 10
1
vote
1
reply
660
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 16 months ago by 68k • written 16 months ago by ▴ 30
5
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13
replies
3.6k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
16 months ago fernanda.backsouza ▴ 30
4
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2
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834
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 16 months ago by ★ 4.1k • written 17 months ago by ▴ 30
2
votes
4
replies
2.1k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 17 months ago by • 0
2
votes
2
replies
698
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 19 months ago by ★ 4.1k • written 19 months ago by • 0
0
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0
replies
787
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
22 months ago mch • 0
0
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4
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3.7k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 11 months ago by • 0 • written 24 months ago by • 0
3
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2
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2.7k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by ▴ 10
0
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0
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742
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
2.2 years ago georgii.vdovin • 0
1
vote
4
replies
2.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
2.2 years ago Jiyoung Lee • 0
0
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1
reply
997
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 2.3 years ago by 43k • written 2.3 years ago by • 0
0
votes
5
replies
2.7k
views
enrichKEGG function error
cluster clusterProfiler KEGG
2.4 years ago • updated 2.3 years ago ruba-mahmoud • 0
1
vote
3
replies
2.2k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 10
0
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13
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13k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.5 years ago Laia ▴ 10
0
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5
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2.2k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 2.5 years ago by • 0
4
votes
11
replies
5.2k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 2.3 years ago by • 0 • written 2.5 years ago by ▴ 10
4
votes
2
replies
7.1k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 2.5 years ago by ▴ 50 • written 2.5 years ago by • 0
1
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7
replies
3.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by ▴ 10
2
votes
6
replies
4.5k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 20 months ago by ★ 4.1k • written 2.5 years ago by ▴ 10
1
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3
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1.9k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 2.7 years ago by 68k • written 2.8 years ago by • 0
4
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2
replies
5.0k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
2.9 years ago Wuschel ▴ 10
0
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2
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1.1k
views
Shivani
kegg
updated 2.9 years ago by ▴ 60 • written 2.9 years ago by • 0
4
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6
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5.6k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 3.0 years ago by ★ 4.1k • written 3.2 years ago by ▴ 10
3
votes
13
replies
3.9k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.1 years ago • updated 2.6 years ago nute11a ▴ 10
0
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3
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1.5k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
3.1 years ago abf ▴ 30
1
vote
1
reply
1.8k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 20
0
votes
2
replies
1.4k
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 3.1 years ago by ▴ 70 • written 3.1 years ago by ▴ 20
1
vote
3
replies
3.0k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 19 months ago by • 0 • written 3.3 years ago by • 0
0
votes
2
replies
4.1k
views
KEGG Pathway in R
keggrespathways KEGG
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by • 0
0
votes
1
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1.3k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.4 years ago by 43k • written 3.4 years ago by • 0
0
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1
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1.9k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 3.6 years ago by ★ 4.0k • written 3.6 years ago by • 0
0
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0
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1.2k
views
Editing KEGG pathways in R
KEGG
3.9 years ago Jordan • 0
1
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0
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2.1k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
3.9 years ago makrez ▴ 10
1
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0
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1.9k
views
documentation on clusterProfiler output
clusterProfiler KEGG
3.9 years ago rafaela.perez ▴ 10
0
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6
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6.6k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
4.1 years ago Bogdan ▴ 670
0
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2
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2.8k
views
Can't install KEGGprofile
KEGG RNASeq
updated 4.3 years ago by 68k • written 4.3 years ago by • 0
0
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0
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1.5k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
4.5 years ago jol.espinoz ▴ 40
6
votes
5
replies
2.2k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.5 years ago by ★ 1.6k • written 4.5 years ago by • 0
2
votes
2
replies
1.6k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
0
votes
3
replies
1.6k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 670
0
votes
1
reply
2.6k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 5.4 years ago by 25k • written 5.4 years ago by • 0
113 results • Page 1 of 3
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Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k
I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
Comment: Average biological replicates in RNA-seq by boczniak767 ▴ 740
@atpoint Should I first standardise data and then average replicates?
Comment: 3-factor DESeq2 trime-series analysis by gogeni5529 • 0
Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…
Comment: 3-factor DESeq2 trime-series analysis by swbarnes2 ★ 1.4k
What does your PCA look like? A lot of times, I find that different cell lines are so different from each other, that they should not be d…
Comment: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by yongjie.wang • 0
Thanks for your reply. " normFactors <- exp(-1 * offst(set2)) normFactors <- normFactors / exp(rowMeans(log(normFactors))) normalizat…
Votes
Answer: Limpa Pipeline Order
A: How barcode-plot enrichment is calculated?
A: How barcode-plot enrichment is calculated?
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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