Showing : Kegg • reset
0
votes
13
replies
5.8k
views
gage pathways enrichment analysis
gage pathways kegg
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
3
votes
13
replies
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 14 months ago nute11a ▴ 10
0
votes
13
replies
4.4k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
12 months ago Laia ▴ 10
4
votes
11
replies
2.4k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 10 months ago by • 0 • written 13 months ago by ▴ 10
7
votes
11
replies
2.5k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 6.1 years ago by 50k • written 6.1 years ago by ▴ 60
1
vote
9
replies
2.8k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 6.0 years ago by ▴ 10 • written 6.0 years ago by ▴ 20
2
votes
8
replies
2.4k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq KEGG
7.2 years ago Xavier ▴ 10
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 13 months ago by ▴ 750 • written 13 months ago by • 0
6
votes
6
replies
5.0k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 4.2 years ago by 50k • written 4.2 years ago by ▴ 50
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 8.4 years ago by 50k • written 8.4 years ago by ▴ 830
2
votes
6
replies
1.9k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 3 months ago by ★ 3.9k • written 13 months ago by • 0
0
votes
6
replies
3.6k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.7 years ago Bogdan ▴ 670
4
votes
6
replies
3.6k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 19 months ago by ★ 3.9k • written 22 months ago by ▴ 10
4
votes
6
replies
3.0k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
8.9 years ago alakatos ▴ 130
1
vote
5
replies
2.9k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.7 years ago by • 0 • written 5.7 years ago by ▴ 40
0
votes
5
replies
2.6k
views
How to use topGO and KEGG with de-novo species
topgo edger limma kegga kegg
updated 6.6 years ago by 50k • written 6.6 years ago by ▴ 10
0
votes
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 13 months ago by • 0
0
votes
5
replies
2.6k
views
Gene Symbol with Pathview
pathview bioconductor kegg visualization
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by • 0
0
votes
5
replies
1.9k
views
Gene set enrichment analysis for GO categories and KEGG pathway
GO KEGG
8.4 years ago libya.tahani • 0
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
12 months ago • updated 11 months ago ruba-mahmoud • 0
6
votes
5
replies
1.5k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.1 years ago by ★ 1.6k • written 3.1 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 6.7 years ago by 50k • written 6.7 years ago by ▴ 30
4
votes
4
replies
1.7k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.4 years ago AZ ▴ 30
1
vote
4
replies
883
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
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
1
vote
4
replies
996
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
10 months ago Jiyoung Lee • 0
5
votes
4
replies
1.6k
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 9.5 years ago by 50k • written 9.6 years ago by ▴ 120
2
votes
3
replies
4.8k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 2.7 years ago by • 0 • written 8.3 years ago by ▴ 20
1
vote
3
replies
2.2k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 6.5 years ago by ▴ 40 • written 7.1 years ago by ▴ 30
1
vote
3
replies
1.2k
views
Ortholog conversions of non-model organisms not present in Biomart, ensembl or KEGG
rnaseq_analysis KEGG nonmodel species
updated 5.6 years ago by 65k • written 5.6 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 12 months ago by ★ 3.9k • written 12 months ago by ▴ 10
0
votes
3
replies
1.1k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 6 months ago by ▴ 20 • written 6 months ago by • 0
0
votes
3
replies
931
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
20 months ago abf ▴ 30
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 8 weeks ago by • 0 • written 22 months ago by • 0
1
vote
3
replies
1.1k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 15 months ago by 65k • written 16 months ago by • 0
0
votes
3
replies
1.1k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 3.9 years ago by 65k • written 3.9 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
8.0 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 • updated 8.1 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
6.4 years ago ladypurrsia ▴ 10
1
vote
2
replies
1.8k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 7.8 years ago by ★ 1.2k • written 9.4 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
6.6 years ago mictadlo ▴ 10
0
votes
2
replies
2.2k
views
Accessing KEGG (errors w/ KEGGREST)
KEGG keggrest
updated 7.2 years ago by 50k • written 7.2 years ago by • 0
0
votes
2
replies
1.7k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 9.1 years ago by ★ 1.6k • written 9.1 years ago by ▴ 100
0
votes
2
replies
884
views
how can I find a pathway
kegg KEGGREST
4.4 years ago Bioinformatics ▴ 30
0
votes
2
replies
2.1k
views
Can't install KEGGprofile
KEGG RNASeq
updated 2.9 years ago by 65k • written 2.9 years ago by • 0
0
votes
2
replies
1.3k
views
Retrieve KEGG from protein GI
R KEGG KEGGREST
7.3 years ago felipelira3 • 0
3
votes
2
replies
1.0k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
0
votes
2
replies
1.7k
views
Drawing custom KEGG pathways
pathview KEGG
2.9 years ago curiousmind007 ▴ 10
50 results • Page 1 of 1
Recent ...
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Answer: Memory errors using read.bismark? by Peter Hickey ▴ 690
Thanks for sharing an example file. This is a very large non-CpG methylation dataset, which are tricky to work with for a number of reason…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by Peter Hickey ▴ 690
Superficially, your issue is similar to [https://github.com/hansenlab/bsseq/issues/136](https://github.com/hansenlab/bsseq/issues/136). You…
Answer: Reading huge bismark coverage files using bbseq::read.bismark by Peter Hickey ▴ 690
I'm one of the **bsseq** developers. Are you able to share one of your files with me (e.g., via Dropbox, Google Drive, OneDrive, etc.). Tha…
Comment: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var by daniel.carbajo • 0
Yeah I think this is the way to go! How can I pass `col_list` here though? `Heatmap` does not accept a list of color vectors... How can I m…
Answer: The issue with SGSeq_analyzeFeatures() returns errors on BAM files by kamryncole1963 • 0
https://support.bioconductor.org/p/85837/[tunnel rush][1] Refer to this link, it may help. [1]: https://tunnelrush3.com
Votes
Answer: ComplexHeatmap: add pch to rowAnnotation when the input is a data frame with var
Comment: Not fully paired differential gene expression analysis
Answer: GSVA error
Comment: DESeq2 - Plot Nr. Genes vs Variance explained in PCA
Answer: How to retrieve detailed regression results from deseq2
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