Showing : KEGG • reset
0
votes
0
replies
32
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
10 hours ago Fred • 0
0
votes
5
replies
250
views
enrichKEGG function error
cluster clusterProfiler KEGG
5 weeks ago • updated 18 days ago ruba-mahmoud • 0
1
vote
3
replies
208
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 7 weeks ago by ★ 3.6k • written 7 weeks ago by ▴ 10
0
votes
13
replies
601
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
9 weeks ago Laia ▴ 10
0
votes
3
replies
289
views
[limma::kegga] Pathway names all NA
KEGG limma
updated 9 weeks ago by 47k • written 9 weeks ago by • 0
2
votes
11
replies
699
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 7 days ago by • 0 • written 11 weeks ago by ▴ 10
4
votes
2
replies
1.1k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 12 weeks ago by ▴ 50 • written 12 weeks ago by • 0
1
vote
7
replies
490
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 12 weeks ago by ▴ 720 • written 3 months ago by • 0
1
vote
4
replies
375
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
3 months ago • updated 12 weeks ago ruiqi.li • 0
1
vote
3
replies
463
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 5 months ago by 62k • written 6 months ago by • 0
4
votes
2
replies
463
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
7 months ago Wuschel ▴ 10
0
votes
2
replies
308
views
Shivani
kegg
updated 7 months ago by ▴ 30 • written 7 months ago by • 0
4
votes
6
replies
1.8k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 9 months ago by ★ 3.6k • written 11 months ago by ▴ 10
0
votes
13
replies
1.2k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
9 months ago • updated 3 months ago nute11a • 0
0
votes
3
replies
496
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
9 months ago abf ▴ 30
1
vote
1
reply
584
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 9 months ago by 62k • written 9 months ago by ▴ 20
0
votes
2
replies
445
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 10 months ago by ▴ 70 • written 10 months ago by ▴ 20
0
votes
2
replies
850
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 9 weeks ago by • 0 • written 11 months ago by • 0
0
votes
2
replies
2.3k
views
KEGG Pathway in R
keggrespathways KEGG
updated 12 months ago by 3.8k • written 12 months ago by • 0
0
votes
1
reply
419
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 13 months ago by 40k • written 13 months ago by • 0
0
votes
1
reply
757
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 16 months ago by 3.8k • written 16 months ago by • 0
0
votes
0
replies
496
views
Editing KEGG pathways in R
KEGG
19 months ago Jordan • 0
0
votes
0
replies
816
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
19 months ago makrez • 0
1
vote
0
replies
740
views
documentation on clusterProfiler output
clusterProfiler KEGG
20 months ago rafaela.perez ▴ 10
0
votes
6
replies
2.4k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
22 months ago Bogdan ▴ 660
0
votes
2
replies
1.1k
views
Drawing custom KEGG pathways
pathview KEGG
2.0 years ago • updated 24 months ago curiousmind007 ▴ 10
0
votes
2
replies
1.5k
views
Can't install KEGGprofile
KEGG RNASeq
updated 2.0 years ago by 62k • written 2.0 years ago by • 0
0
votes
0
replies
595
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
2.2 years ago jol.espinoz ▴ 40
6
votes
5
replies
1.0k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 2.2 years ago by ★ 1.6k • written 2.2 years ago by • 0
2
votes
2
replies
683
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 2.5 years ago by 62k • written 2.5 years ago by • 0
0
votes
3
replies
684
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 3.0 years ago by 62k • written 3.0 years ago by ▴ 660
0
votes
1
reply
986
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 3.1 years ago by 25k • written 3.1 years ago by • 0
2
votes
2
replies
757
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 3.2 years ago by 62k • written 3.2 years ago by ▴ 10
0
votes
0
replies
470
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
3.2 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
810
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 3.3 years ago by 47k • written 3.7 years ago by ▴ 50
6
votes
6
replies
4.2k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 3.3 years ago by 47k • written 3.3 years ago by ▴ 50
0
votes
0
replies
547
views
gage function problem in R
gage R kegg pathview
updated 3.3 years ago by 40k • written 3.3 years ago by • 0
4
votes
4
replies
993
views
How I interpret this plot from pathview
pathview kegg r pathway
3.5 years ago AZ ▴ 30
0
votes
2
replies
593
views
how can I find a pathway
kegg KEGGREST
3.5 years ago Bioinformatics ▴ 30
0
votes
0
replies
688
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
3.6 years ago MimR • 0
0
votes
0
replies
530
views
pvaluecutoff meaning in enrichKEGG
KEGG RNAseq
3.7 years ago sportiellomike • 0
0
votes
0
replies
680
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview Gene Mapping KEGG
3.7 years ago omarrafiqued ▴ 50
0
votes
2
replies
835
views
Issue with xml files downloaded with `pathview()`
pathview kegg xml
updated 3.9 years ago by ★ 1.6k • written 3.9 years ago by ▴ 10
5
votes
4
replies
1.1k
views
Function kegga not working for species other than the conventional ones - Pathways do not overlap with universe
kegga limma pathway analysis kegg
updated 4.1 years ago by 47k • written 4.1 years ago by ▴ 60
0
votes
0
replies
540
views
How to integrate and visualize RNASeq / Proteomics data for metabolomics pathways?
r metabolomics KEGG Proteomics Transcriptomics
4.2 years ago Wuschel ▴ 10
0
votes
0
replies
557
views
Help with mapping Kegg hsa01100 using pathview
kegg pathway pathview
4.2 years ago Ahdee ▴ 50
0
votes
1
reply
1.0k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 17 days ago by • 0 • written 4.6 years ago by • 0
0
votes
0
replies
698
views
Pathview input error: non-numeric variable in data frame
pathview kegg pathways package
4.7 years ago anc.informatics • 0
1
vote
4
replies
610
views
How to apply KEGG enrichment analysis to the overlap of multiple contrasts in MArrayLM fit?
limma kegg
updated 4.7 years ago by 47k • written 4.7 years ago by ▴ 10
1
vote
3
replies
919
views
Ortholog conversions of non-model organisms not present in Biomart, ensembl or KEGG
rnaseq_analysis KEGG nonmodel species
updated 4.7 years ago by 62k • written 4.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Trouble Loading Data into Champ by hfbarrerat • 0
Try myLoad <- champ.load("raw/",arraytype="EPIC")
Comment: BiocGenerics binary is outdated for macOS ARM by jennifer.wokaty ▴ 60
Thanks, Mike, for posting about this and thanks to Lori for noticing the lock. I removed it and RProtoBufLib passes R CMD check. Unfortunat…
Comment: BiocGenerics binary is outdated for macOS ARM by Michael Steinbaugh ▴ 90
Ah thanks for the update. Yeah I see that the flowClust release is the culprit: https://www.bioconductor.org/packages/release/bioc/html/flo…
Comment: Submitting BSgenome package for a new assembly by Manish • 0
Thanks for the info. This is very helpful. -Manish
Comment: Merge 2 accounts, or delete 1 account. by shepherl 3.5k
are you talking specifically on the support site or elsewhere also?
Votes
flowCore: using read.FCS with which.lines is not time efficient?
Comment: BiocGenerics binary is outdated for macOS ARM
Comment: Submitting BSgenome package for a new assembly
How to create "trait data" file for WGCNA
Comment: Visualization of negative log CPM values
Awards • All
Popular Question to kevin.rue ▴ 320
Popular Question to Miss Agnieszka Aleksandra Golicz ▴ 40
Popular Question to shepherl 3.5k
Popular Question to boczniak767 ▴ 720
Scholar to Gordon Smyth 47k
Locations • All
Colombia, just now
United States, 5 minutes ago
United States, 14 minutes ago
The city by the bay, 41 minutes ago
United States, 46 minutes ago
Traffic: 572 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