Showing : KEGG • reset
2
votes
2
replies
135
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How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
5 days ago julia_mcdonough • 0
2
votes
2
replies
229
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 8 weeks ago by ★ 3.9k • written 8 weeks ago by • 0
0
votes
0
replies
334
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
5 months ago mch • 0
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 7 months ago by • 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
0
replies
335
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 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
0
votes
1
reply
545
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 10 months ago by 41k • written 10 months ago by • 0
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
12 months ago • updated 11 months ago ruba-mahmoud • 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
13
replies
4.5k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
13 months ago Laia ▴ 10
0
votes
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 13 months ago by • 0
4
votes
11
replies
2.4k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 11 months ago by • 0 • written 13 months ago by ▴ 10
4
votes
2
replies
4.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 13 months ago by ▴ 50 • written 13 months ago by • 0
1
vote
7
replies
1.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 13 months ago by ▴ 760 • written 13 months ago by • 0
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
1
vote
3
replies
1.1k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 16 months ago by 65k • written 16 months ago by • 0
4
votes
2
replies
1.8k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
18 months ago Wuschel ▴ 10
0
votes
2
replies
656
views
Shivani
kegg
updated 18 months ago by ▴ 30 • written 18 months ago by • 0
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
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
3
replies
933
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
20 months ago abf ▴ 30
1
vote
1
reply
1.2k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 20 months ago by 65k • written 20 months ago by ▴ 20
0
votes
2
replies
836
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 20 months ago by ▴ 70 • written 21 months ago by ▴ 20
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
0
votes
2
replies
3.3k
views
KEGG Pathway in R
keggrespathways KEGG
updated 22 months ago by ★ 3.9k • written 22 months ago by • 0
0
votes
1
reply
800
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.0 years ago by 41k • written 2.0 years ago by • 0
0
votes
1
reply
1.2k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.2 years ago by ★ 3.9k • written 2.2 years ago by • 0
0
votes
0
replies
790
views
Editing KEGG pathways in R
KEGG
2.5 years ago Jordan • 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
2.5 years ago rafaela.perez ▴ 10
0
votes
6
replies
3.6k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.7 years ago Bogdan ▴ 670
0
votes
2
replies
1.8k
views
Drawing custom KEGG pathways
pathview KEGG
2.9 years ago curiousmind007 ▴ 10
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
0
replies
975
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.1 years ago jol.espinoz ▴ 40
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
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
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
1
reply
1.7k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.0 years ago by 25k • written 4.0 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
0
votes
0
replies
763
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
1.1k
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
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
0
votes
0
replies
863
views
gage function problem in R
gage R kegg pathview
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
4
votes
4
replies
1.7k
views
How I interpret this plot from pathview
pathview kegg r pathway
4.4 years ago AZ ▴ 30
0
votes
2
replies
884
views
how can I find a pathway
kegg KEGGREST
4.4 years ago Bioinformatics ▴ 30
0
votes
0
replies
941
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
4.5 years ago MimR • 0
0
votes
0
replies
808
views
pvaluecutoff meaning in enrichKEGG
KEGG RNAseq
4.6 years ago sportiellomike • 0
0
votes
0
replies
961
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview Gene Mapping KEGG
4.6 years ago omarrafiqued ▴ 50
0
votes
2
replies
1.1k
views
Issue with xml files downloaded with `pathview()`
pathview kegg xml
updated 4.7 years ago by ★ 1.6k • written 4.8 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: DESeq filtering specific to contrasts by Carlin95 • 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark by jacques.imbert • 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist by Basti ▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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