Showing : KEGG • reset
0
votes
13
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5.0k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
14 months ago Laia ▴ 10
3
votes
13
replies
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
2
votes
13
replies
481
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
27 days ago • updated 24 days ago fernanda.backsouza ▴ 10
0
votes
13
replies
5.9k
views
gage pathways enrichment analysis
gage pathways kegg
updated 9.5 years ago by ★ 1.6k • written 9.5 years ago by ▴ 100
7
votes
11
replies
2.6k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.2 years ago by 50k • written 6.2 years ago by ▴ 60
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
1
vote
9
replies
2.9k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 6.1 years ago by ▴ 10 • written 6.1 years ago by ▴ 20
2
votes
8
replies
2.5k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq KEGG
7.3 years ago Xavier ▴ 10
1
vote
7
replies
1.9k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
4
votes
6
replies
3.1k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
9.0 years ago • updated 8.9 years ago alakatos ▴ 130
7
votes
6
replies
3.2k
views
Interpretation of mroast gene set analysis in R and appropriate use of the function barcode plot regarding a microarray dataset
limma mroast barcodeplot KEGG gene set testing
updated 8.5 years ago by 50k • written 8.5 years ago by ▴ 830
2
votes
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
6
votes
6
replies
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
4
votes
6
replies
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
0
votes
6
replies
3.8k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.8 years ago Bogdan ▴ 670
0
votes
5
replies
2.7k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 8.6 years ago by ★ 1.6k • written 8.6 years ago by • 0
0
votes
5
replies
2.7k
views
How to use topGO and KEGG with de-novo species
topgo edger limma kegga kegg
updated 6.7 years ago by 50k • written 6.7 years ago by ▴ 10
0
votes
5
replies
1.9k
views
Gene set enrichment analysis for GO categories and KEGG pathway
GO KEGG
8.5 years ago • updated 8.4 years ago libya.tahani • 0
0
votes
5
replies
1.4k
views
enrichKEGG function error
cluster clusterProfiler KEGG
13 months ago • updated 12 months ago ruba-mahmoud • 0
1
vote
5
replies
3.0k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.8 years ago by • 0 • written 5.8 years ago by ▴ 40
0
votes
5
replies
1.3k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 14 months ago by • 0
6
votes
5
replies
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
votes
4
replies
1.7k
views
Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 6.8 years ago by 50k • written 6.8 years ago by ▴ 30
1
vote
4
replies
911
views
How to apply KEGG enrichment analysis to the overlap of multiple contrasts in MArrayLM fit?
limma kegg
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 10
4
votes
4
replies
1.8k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.5 years ago AZ ▴ 30
1
vote
4
replies
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
11 months ago Jiyoung Lee • 0
1
vote
4
replies
1.5k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 7.2 years ago by ▴ 100 • written 7.2 years ago by • 0
5
votes
4
replies
1.7k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 60
4
votes
4
replies
7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 9.6 years ago by 50k • written 9.7 years ago by ▴ 120
2
votes
3
replies
4.9k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 2.8 years ago by • 0 • written 8.4 years ago by ▴ 20
1
vote
3
replies
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
1
vote
3
replies
2.2k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 6.6 years ago by ▴ 40 • written 7.2 years ago by ▴ 30
1
vote
3
replies
1.3k
views
Ortholog conversions of non-model organisms not present in Biomart, ensembl or KEGG
rnaseq_analysis KEGG nonmodel species
updated 5.7 years ago by 65k • written 5.7 years ago by • 0
1
vote
3
replies
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
0
votes
3
replies
1.2k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 7 months ago by ▴ 20 • written 8 months ago by • 0
0
votes
3
replies
969
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
21 months ago abf ▴ 30
1
vote
3
replies
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
votes
3
replies
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
votes
3
replies
1.4k
views
kegga error from edgeR
edger r bioconductor pathway analysis kegg
updated 6.2 years ago by 50k • written 6.2 years ago by ▴ 110
0
votes
3
replies
1.4k
views
CHiPpeakAnno GO and/or KEGG results presenting
chippeakanno go kegg graphics
8.1 years ago lokapal • 0
1
vote
3
replies
1.6k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.2 years ago serpalma.v ▴ 60
1
vote
2
replies
2.4k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
6.5 years ago ladypurrsia ▴ 10
1
vote
2
replies
1.9k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 7.9 years ago by ★ 1.2k • written 9.5 years ago by ▴ 100
0
votes
2
replies
1.2k
views
how to build gene.pathway data.frame for non-model organism
limma kegg topgo dataframe edger
6.7 years ago mictadlo ▴ 10
0
votes
2
replies
2.3k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 7.3 years ago by 50k • written 7.3 years ago by • 0
0
votes
2
replies
1.8k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 100
0
votes
2
replies
914
views
how can I find a pathway
kegg KEGGREST
4.5 years ago Bioinformatics ▴ 30
0
votes
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
votes
2
replies
1.3k
views
Retrieve KEGG from protein GI
R KEGG KEGGREST
7.4 years ago felipelira3 • 0
3
votes
2
replies
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
50 results • Page 1 of 1
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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?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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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