Showing : Kegg • reset
7
votes
6
replies
2.6k
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 7.2 years ago by 47k • written 7.2 years ago by ▴ 800
7
votes
11
replies
1.8k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 4.9 years ago by 47k • written 4.9 years ago by ▴ 50
6
votes
6
replies
3.7k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 2.9 years ago by 47k • written 2.9 years ago by ▴ 50
6
votes
5
replies
877
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 22 months ago by ★ 1.6k • written 22 months ago by • 0
5
votes
4
replies
917
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 3.7 years ago by 47k • written 3.7 years ago by ▴ 60
4
votes
4
replies
7.0k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 8.3 years ago by 47k • written 8.4 years ago by ▴ 120
4
votes
6
replies
1.2k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 4 months ago by ★ 3.5k • written 7 months ago by ▴ 10
4
votes
6
replies
2.4k
views
A good alternative for RDavidWebService ??
functional annotation KEGG RDavidWebService
7.6 years ago alakatos ▴ 120
4
votes
4
replies
808
views
How I interpret this plot from pathview
pathview kegg r pathway
3.2 years ago AZ ▴ 30
4
votes
2
replies
218
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
3 months ago Wuschel ▴ 10
3
votes
1
reply
723
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 2.9 years ago by 47k • written 3.3 years ago by ▴ 50
2
votes
8
replies
1.8k
views
GOseq package: Which genes are included in the "numDEInCat"?
GOseq KEGG
6.0 years ago Xavier ▴ 10
2
votes
4
replies
984
views
Can't find gene list for KEGG genesets
kegg geneset genelist gage package
updated 5.4 years ago by 47k • written 5.4 years ago by ▴ 30
2
votes
2
replies
555
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 2.9 years ago by 62k • written 2.9 years ago by ▴ 10
2
votes
3
replies
3.5k
views
Pathview None of the genes or compounds mapped to the pathway
pathview pathways KEGG empty map
updated 18 months ago by • 0 • written 7.1 years ago by ▴ 20
2
votes
2
replies
587
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 2.1 years ago by 62k • written 2.1 years ago by • 0
2
votes
1
reply
806
views
elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 7.2 years ago by 62k • written 7.2 years ago by ▴ 40
1
vote
1
reply
1.6k
views
Using pathview with uncommon species leads to Errors
pathview Kegg rnaseq data visualization
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by • 0
1
vote
0
replies
461
views
documentation on clusterProfiler output
clusterProfiler KEGG
15 months ago rafaela.perez ▴ 10
1
vote
3
replies
800
views
Ortholog conversions of non-model organisms not present in Biomart, ensembl or KEGG
rnaseq_analysis KEGG nonmodel species
updated 4.4 years ago by 62k • written 4.4 years ago by • 0
1
vote
4
replies
516
views
How to apply KEGG enrichment analysis to the overlap of multiple contrasts in MArrayLM fit?
limma kegg
updated 4.3 years ago by 47k • written 4.3 years ago by ▴ 10
1
vote
3
replies
240
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 4 weeks ago by 62k • written 8 weeks ago by • 0
1
vote
4
replies
1.0k
views
Indirect path in KEGG, activation or inhibition?
bioconductor graphite kegg pathway analysis
updated 5.9 years ago by ▴ 100 • written 5.9 years ago by • 0
1
vote
3
replies
1.6k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview kegg error bioconductor rnaseq
updated 5.2 years ago by ▴ 40 • written 5.9 years ago by ▴ 30
1
vote
1
reply
915
views
embed url in pathview images
pathview r pdf kegg graphviz
updated 7.1 years ago by ★ 1.6k • written 7.1 years ago by • 0
1
vote
2
replies
1.8k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview KEGG parsing
5.2 years ago ladypurrsia ▴ 10
1
vote
1
reply
949
views
Highlight ECs by KEGG module
pathview KEGG
updated 5.2 years ago by ★ 1.6k • written 5.2 years ago by • 0
1
vote
3
replies
1.1k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
6.9 years ago serpalma.v ▴ 60
1
vote
0
replies
622
views
EGSEA install licensed KEGG data
EGSEA KEGG EGSEAdata
5.0 years ago john.thompson ▴ 10
1
vote
2
replies
944
views
How to get the latest KEGG pathway
KEGG kegg.db kegggraph
5.0 years ago Raymond ▴ 20
1
vote
2
replies
1.4k
views
GeneAnswer for bacteria metagenomes
geneanswers metagenome kegg
updated 6.6 years ago by ★ 1.2k • written 8.2 years ago by ▴ 80
1
vote
1
reply
903
views
How can get the GO and KEGG miRNA microarray Agilent?
go kegg limma microarray mirna
7.4 years ago santi.cabellos ▴ 10
1
vote
1
reply
669
views
Gene Set Enrichment based on gene presence/absence
gene set enrichment KEGG
updated 4.9 years ago by ▴ 700 • written 4.9 years ago by ▴ 10
1
vote
1
reply
373
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 5 months ago by 62k • written 5 months ago by • 0
1
vote
0
replies
610
views
How to find back the list of genes involved in pathways produced by a kegg analysis (kegga) with limma package
edger kegg
4.9 years ago jambroise83 ▴ 10
1
vote
9
replies
1.8k
views
Gene-Metabolite and Metabolite-Pathway network from KEGG with KEGGREST
KEGG keggrest
updated 4.8 years ago by ▴ 10 • written 4.8 years ago by ▴ 20
1
vote
1
reply
589
views
kegg orthology entry to pathway ko
kegg
updated 4.7 years ago by 62k • written 4.7 years ago by ▴ 10
1
vote
5
replies
2.1k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 18 months ago by • 0 • written 4.5 years ago by ▴ 20
0
votes
0
replies
374
views
Editing KEGG pathways in R
KEGG
15 months ago Jordan • 0
0
votes
10
replies
637
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
updated 4 months ago by ★ 3.5k • written 5 months ago by • 0
0
votes
2
replies
1.2k
views
Can't install KEGGprofile
KEGG RNASeq
updated 20 months ago by 62k • written 20 months ago by • 0
0
votes
2
replies
319
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 6 months ago by ▴ 70 • written 6 months ago by • 0
0
votes
2
replies
159
views
Shivani
kegg
updated 3 months ago by ▴ 30 • written 3 months ago by • 0
0
votes
0
replies
572
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
15 months ago makrez • 0
0
votes
6
replies
1.7k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
18 months ago • updated 17 months ago Bogdan ▴ 660
0
votes
2
replies
1.9k
views
KEGG Pathway in R
keggrespathways KEGG
updated 7 months ago by 3.7k • written 7 months ago by • 0
0
votes
3
replies
331
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
5 months ago abf ▴ 30
0
votes
1
reply
484
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 7 weeks ago by • 0 • written 7 months ago by • 0
0
votes
0
replies
595
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview Gene Mapping KEGG
3.4 years ago omarrafiqued ▴ 50
0
votes
2
replies
6.3k
views
Using Keggrest to convert ncbi gene IDs to kegg orthology and pathway
keggrest kegg keggorthology
updated 8.2 years ago by 62k • written 8.2 years ago by ▴ 80
50 results • Page 1 of 1
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Replies
Comment: transcript name mapping between human and mouse by Eric • 0
It works very well, and thanks for such a great answer! Because I use the old version gtf from GENECODE (vM12), the id version does not mat…
Comment: How to normalize long-read RNA-seq data for comparison with short-reads by Bernardo • 0
Just did that, thank you for the suggestion.
Comment: Empty ChipQC Report by Okan • 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by Gordon Smyth 47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper by k.roelfs • 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Votes
Answer: transcript name mapping between human and mouse
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
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