Showing : Kegg • reset
7
votes
11
replies
2.6k
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
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
5.0k
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
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
3.6k
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
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 14 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
165
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 4 days ago by ★ 3.9k • written 6 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 8.3 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
1.0k
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
1.9k
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
237
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 9 weeks ago by ★ 3.9k • written 9 weeks ago by • 0
2
votes
2
replies
169
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
14 days ago • updated 13 days ago julia_mcdonough • 0
2
votes
8
replies
2.4k
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 • updated 6.4 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
278
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
4 days ago • updated 1 day 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 6.4 years ago by ★ 1.6k • written 6.4 years ago by • 0
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
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
1.0k
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
1.2k
views
documentation on clusterProfiler output
clusterProfiler KEGG
2.6 years ago rafaela.perez ▴ 10
1
vote
1
reply
63
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 2 days ago by 65k • written 2 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
2.9k
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
976
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 6.0 years ago by ▴ 20
1
vote
0
replies
907
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
890
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
995
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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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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