Showing : KEGG • reset
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
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
6
votes
6
replies
5.1k
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
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
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
6
replies
3.1k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
8.9 years ago alakatos ▴ 130
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
4
votes
2
replies
4.4k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 14 months ago by ▴ 50 • written 14 months ago by • 0
4
votes
11
replies
2.5k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 11 months ago by • 0 • written 13 months ago by ▴ 10
4
votes
4
replies
1.7k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.5 years ago • updated 4.4 years ago AZ ▴ 30
4
votes
6
replies
3.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 20 months ago by ★ 3.9k • written 22 months ago by ▴ 10
4
votes
2
replies
1.9k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
18 months ago Wuschel ▴ 10
3
votes
1
reply
1.2k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 4.2 years ago by 50k • written 4.6 years ago by ▴ 50
3
votes
13
replies
2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 15 months ago nute11a ▴ 10
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 8 months ago by ★ 3.9k • written 8 months ago by ▴ 10
3
votes
2
replies
206
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 11 days ago by ★ 3.9k • written 13 days ago by ▴ 10
2
votes
3
replies
4.8k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 2.8 years ago by • 0 • written 8.4 years ago by ▴ 20
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
2
votes
1
reply
1.1k
views
elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 40
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 3 months ago by ★ 3.9k • written 14 months ago by ▴ 10
2
votes
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 3.4 years ago by • 0
2
votes
2
replies
1.2k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.1 years ago by 65k • written 4.1 years ago by ▴ 10
2
votes
2
replies
257
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 10 weeks ago by ★ 3.9k • written 10 weeks ago by • 0
2
votes
2
replies
188
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
21 days ago • updated 20 days ago julia_mcdonough • 0
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
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
1
reply
1.2k
views
embed url in pathview images
pathview r pdf kegg graphviz
updated 8.4 years ago by ★ 1.6k • written 8.4 years ago by • 0
1
vote
13
replies
375
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
11 days ago • updated 8 days ago fernanda.backsouza ▴ 10
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 7.2 years ago by ▴ 30
1
vote
1
reply
1.4k
views
Highlight ECs by KEGG module
pathview KEGG
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by • 0
1
vote
2
replies
1.9k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 7.8 years ago by ★ 1.2k • written 9.5 years ago by ▴ 100
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
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
10 months ago Jiyoung Lee • 0
1
vote
0
replies
1.3k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.5 years ago makrez ▴ 10
1
vote
0
replies
1.3k
views
documentation on clusterProfiler output
clusterProfiler KEGG
2.6 years ago rafaela.perez ▴ 10
1
vote
1
reply
105
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 9 days ago by 65k • written 9 days ago by ▴ 10
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 5.6 years ago by 65k • written 5.6 years ago by • 0
1
vote
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
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
1
vote
1
reply
985
views
kegg orthology entry to pathway ko
kegg
updated 5.9 years ago by 65k • written 5.9 years ago by ▴ 10
1
vote
9
replies
2.9k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 6.0 years ago by ▴ 10 • written 6.1 years ago by ▴ 20
1
vote
0
replies
910
views
How to find back the list of genes involved in pathways produced by a kegg analysis (kegga) with limma package
edger kegg
6.1 years ago jambroise83 ▴ 10
1
vote
1
reply
1.9k
views
Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 7.8 years ago by ★ 1.6k • written 7.8 years ago by • 0
1
vote
1
reply
1.1k
views
Gene Set Enrichment based on gene presence/absence
gene set enrichment KEGG
updated 6.2 years ago by ▴ 730 • written 6.2 years ago by ▴ 10
1
vote
1
reply
1.2k
views
How can get the GO and KEGG miRNA microarray Agilent?
go kegg limma microarray mirna
8.6 years ago santi.cabellos ▴ 10
1
vote
4
replies
893
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
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
2.0k
views
How to get the latest KEGG pathway
KEGG kegg.db kegggraph
6.2 years ago Raymond ▴ 20
1
vote
0
replies
1.0k
views
EGSEA install licensed KEGG data
EGSEA KEGG EGSEAdata
6.2 years ago john.thompson ▴ 10
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
50 results • Page 1 of 1
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Replies
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Votes
stuck on unimplemented type 'list' in 'EncodeElement'
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
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