Showing : KEGG • reset
2
votes
13
replies
447
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
19 days ago • updated 16 days ago fernanda.backsouza ▴ 10
1
vote
1
reply
122
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 17 days ago by 65k • written 17 days ago by ▴ 10
3
votes
2
replies
220
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 18 days ago by ★ 3.9k • written 21 days ago by ▴ 10
2
votes
2
replies
203
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
28 days ago julia_mcdonough • 0
2
votes
2
replies
269
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 11 weeks ago by ★ 3.9k • written 12 weeks ago by • 0
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 12 weeks ago by • 0 • written 23 months ago by • 0
2
votes
6
replies
2.0k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 4 months ago by ★ 3.9k • written 14 months ago by ▴ 10
0
votes
1
reply
1.5k
views
ClusterProfiler - enrichKEGG on specific pathways
kegg enrichkegg clusterprofiler
updated 5 months ago by • 0 • written 5.8 years ago by ▴ 40
0
votes
0
replies
363
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
6 months ago mch • 0
0
votes
5
replies
1.2k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 13 months ago by • 0
0
votes
3
replies
1.2k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 7 months ago by ▴ 20 • written 7 months ago by • 0
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 9 months ago by ★ 3.9k • written 9 months ago by ▴ 10
0
votes
0
replies
355
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
9 months ago georgii.vdovin • 0
1
vote
4
replies
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
11 months ago • updated 10 months ago Jiyoung Lee • 0
0
votes
1
reply
565
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 11 months ago by 42k • written 11 months ago by • 0
4
votes
11
replies
2.6k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 11 months ago by • 0 • written 14 months ago by ▴ 10
0
votes
1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 12 months ago by • 0 • written 5.5 years ago by • 0
0
votes
5
replies
1.3k
views
enrichKEGG function error
cluster clusterProfiler KEGG
12 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 13 months ago by ★ 3.9k • written 13 months ago by ▴ 10
0
votes
13
replies
4.9k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
13 months ago Laia ▴ 10
1
vote
7
replies
1.9k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
4
votes
2
replies
4.5k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 14 months ago by ▴ 50 • written 14 months ago by • 0
3
votes
13
replies
2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
21 months ago • updated 15 months ago nute11a ▴ 10
1
vote
3
replies
1.2k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 16 months ago by 65k • written 17 months ago by • 0
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
0
votes
2
replies
687
views
Shivani
kegg
updated 18 months ago by ▴ 40 • written 18 months ago by • 0
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
0
votes
3
replies
957
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
21 months ago abf ▴ 30
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
0
votes
2
replies
865
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 21 months ago by ▴ 70 • written 21 months ago by ▴ 20
0
votes
2
replies
3.3k
views
KEGG Pathway in R
keggrespathways KEGG
updated 23 months ago by ★ 3.9k • written 23 months ago by • 0
0
votes
1
reply
840
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.1 years ago by 42k • written 2.1 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 2.3 years ago by ★ 3.9k • written 2.3 years ago by • 0
0
votes
0
replies
821
views
Editing KEGG pathways in R
KEGG
2.5 years ago Jordan • 0
1
vote
0
replies
1.4k
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
0
votes
6
replies
3.7k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.8 years ago Bogdan ▴ 670
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
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
0
votes
2
replies
1.8k
views
Drawing custom KEGG pathways
pathview KEGG
3.0 years ago • updated 2.9 years ago curiousmind007 ▴ 10
0
votes
2
replies
2.2k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.0 years ago by 65k • written 3.0 years ago by • 0
0
votes
0
replies
1.0k
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 3.2 years ago by ★ 1.6k • written 3.2 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 4.1 years ago by 25k • written 4.1 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
784
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.1 years ago Assa Yeroslaviz ★ 1.5k
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
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
50 results • Page 1 of 1
Recent ...
Replies
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Comment: error by NATASHA • 0
Please ignore, i didnt copy all the scrip
Comment: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you ever find yourself using the `@` function, you should reconsider what you are doing. There are vanishingly small instances when an e…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Here is some example code <https://gist.github.com/mikelove/cbbc84634b6854c865cb5eb08ad9b245>
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Awards • All
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Locations • All
France, just now
UPF, Barcelona, Spain, 1 hour ago
Canada, 1 hour ago
WEHI, Melbourne, Australia, 2 hours ago
San Diego, 2 hours ago
Traffic: 597 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6