Showing : KEGG • reset
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42
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
3 days ago danalvoronov ▴ 10
1
vote
1
reply
132
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 25 days ago by 65k • written 25 days ago by ▴ 10
2
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13
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481
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Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
27 days ago • updated 24 days ago fernanda.backsouza ▴ 10
3
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2
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231
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Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 26 days ago by ★ 4.0k • written 29 days ago by ▴ 10
2
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2
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214
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
5 weeks ago julia_mcdonough • 0
2
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2
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278
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Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
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0
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375
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
0
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3
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1.3k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 7 months ago by ▴ 20 • written 8 months ago by • 0
3
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2
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1.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 9 months ago by ★ 4.0k • written 9 months ago by ▴ 10
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0
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361
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Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
10 months ago georgii.vdovin • 0
1
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4
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1.1k
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pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
11 months ago Jiyoung Lee • 0
0
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1
reply
576
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DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 11 months ago by 42k • written 11 months ago by • 0
0
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5
replies
1.4k
views
enrichKEGG function error
cluster clusterProfiler KEGG
13 months ago • updated 12 months ago ruba-mahmoud • 0
1
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3
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1.1k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 10
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13
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5.0k
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KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
14 months ago Laia ▴ 10
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5
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1.3k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 14 months ago by • 0
4
votes
11
replies
2.6k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 12 months ago by • 0 • written 14 months ago by ▴ 10
4
votes
2
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4.5k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 14 months ago by ▴ 50 • written 14 months ago by • 0
1
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7
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1.9k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
2
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6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 4 months ago by ★ 4.0k • written 14 months ago by ▴ 10
1
vote
3
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1.2k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 17 months ago by 65k • written 17 months ago by • 0
4
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2
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2.0k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
19 months ago Wuschel ▴ 10
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2
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703
views
Shivani
kegg
updated 19 months ago by ▴ 40 • written 19 months ago by • 0
3
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13
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2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
21 months ago • updated 15 months ago nute11a ▴ 10
0
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3
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969
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
21 months ago abf ▴ 30
1
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1
reply
1.2k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 21 months ago by 65k • written 21 months ago by ▴ 20
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2
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873
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How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 21 months ago by ▴ 70 • written 22 months ago by ▴ 20
4
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6
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3.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 20 months ago by ★ 4.0k • written 23 months ago by ▴ 10
1
vote
3
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1.9k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 3 months ago by • 0 • written 23 months ago by • 0
0
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2
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3.3k
views
KEGG Pathway in R
keggrespathways KEGG
updated 23 months ago by ★ 3.9k • written 23 months ago by • 0
0
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1
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850
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Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.1 years ago by 42k • written 2.1 years ago by • 0
0
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1
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1.3k
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How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.3 years ago by ★ 3.9k • written 2.3 years ago by • 0
0
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0
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827
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Editing KEGG pathways in R
KEGG
2.6 years ago Jordan • 0
1
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0
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1.4k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.6 years ago makrez ▴ 10
1
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0
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1.3k
views
documentation on clusterProfiler output
clusterProfiler KEGG
2.6 years ago rafaela.perez ▴ 10
0
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6
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3.8k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.8 years ago Bogdan ▴ 670
0
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2
replies
2.2k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.0 years ago by 65k • written 3.0 years ago by • 0
0
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2
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1.8k
views
Drawing custom KEGG pathways
pathview KEGG
3.0 years ago curiousmind007 ▴ 10
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0
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1.0k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.2 years ago jol.espinoz ▴ 40
6
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5
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1.6k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.2 years ago by ★ 1.6k • written 3.2 years ago by • 0
2
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2
replies
1.1k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.4 years ago by 65k • written 3.5 years ago by • 0
0
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3
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1.1k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.0 years ago by 65k • written 4.0 years ago by ▴ 670
0
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1
reply
1.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.1 years ago by 25k • written 4.1 years ago by • 0
2
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2
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1.2k
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Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.2 years ago by 65k • written 4.2 years ago by ▴ 10
0
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0
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791
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plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.2 years ago Assa Yeroslaviz ★ 1.5k
6
votes
6
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5.1k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 4.3 years ago by 50k • written 4.3 years ago by ▴ 50
0
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0
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896
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gage function problem in R
gage R kegg pathview
updated 4.3 years ago by 42k • written 4.3 years ago by • 0
0
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2
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914
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how can I find a pathway
kegg KEGGREST
4.5 years ago Bioinformatics ▴ 30
4
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4
replies
1.8k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.5 years ago AZ ▴ 30
0
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0
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969
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KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
4.6 years ago MimR • 0
50 results • Page 1 of 1
Recent ...
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Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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