Showing : Kegg • reset
1
vote
4
replies
347
views
pathview - multiple states
pathview Pathways KEGG
4 weeks ago • updated 29 days ago Philippine • 0
1
vote
2
replies
347
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 3 months ago by ▴ 60 • written 3 months ago by • 0
0
votes
0
replies
327
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
5 months ago cereyredondo • 0
0
votes
3
replies
673
views
pathview error
KEGGgraph KEGG
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
votes
0
replies
258
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
7 months ago danalvoronov ▴ 10
1
vote
1
reply
389
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 8 months ago by 67k • written 8 months ago by ▴ 30
5
votes
13
replies
2.2k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
8 months ago fernanda.backsouza ▴ 30
4
votes
2
replies
552
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 8 months ago by ★ 4.1k • written 8 months ago by ▴ 30
2
votes
3
replies
938
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 7 weeks ago by • 0 • written 8 months ago by • 0
2
votes
2
replies
508
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 10 months ago by ★ 4.1k • written 10 months ago by • 0
0
votes
0
replies
582
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
14 months ago mch • 0
0
votes
4
replies
2.5k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 12 weeks ago by • 0 • written 15 months ago by • 0
3
votes
2
replies
1.9k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 16 months ago by ★ 4.1k • written 16 months ago by ▴ 10
0
votes
0
replies
541
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
17 months ago georgii.vdovin • 0
1
vote
4
replies
1.6k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
18 months ago Jiyoung Lee • 0
0
votes
1
reply
769
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 19 months ago by 43k • written 19 months ago by • 0
0
votes
5
replies
2.1k
views
enrichKEGG function error
cluster clusterProfiler KEGG
20 months ago ruba-mahmoud • 0
1
vote
3
replies
1.7k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 21 months ago by ★ 4.1k • written 21 months ago by ▴ 10
0
votes
13
replies
8.3k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
21 months ago Laia ▴ 10
0
votes
5
replies
1.7k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 21 months ago by • 0
4
votes
11
replies
3.9k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 19 months ago by • 0 • written 22 months ago by ▴ 10
4
votes
2
replies
5.9k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 22 months ago by ▴ 50 • written 22 months ago by • 0
1
vote
7
replies
2.8k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 22 months ago by ▴ 780 • written 22 months ago by ▴ 10
2
votes
6
replies
3.2k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 12 months ago by ★ 4.1k • written 22 months ago by ▴ 10
1
vote
3
replies
1.6k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 2.0 years ago by 67k • written 2.1 years ago by • 0
4
votes
2
replies
3.4k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
2.2 years ago Wuschel ▴ 10
0
votes
2
replies
915
views
Shivani
kegg
updated 2.2 years ago by ▴ 60 • written 2.2 years ago by • 0
4
votes
6
replies
4.6k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.3 years ago by ★ 4.1k • written 2.5 years ago by ▴ 10
3
votes
13
replies
3.2k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.4 years ago • updated 23 months ago nute11a ▴ 10
0
votes
3
replies
1.3k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.4 years ago abf ▴ 30
1
vote
1
reply
1.5k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 2.4 years ago by 67k • written 2.4 years ago by ▴ 20
0
votes
2
replies
1.1k
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 2.4 years ago by ▴ 70 • written 2.4 years ago by ▴ 20
1
vote
3
replies
2.5k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 10 months ago by • 0 • written 2.6 years ago by • 0
0
votes
2
replies
3.8k
views
KEGG Pathway in R
keggrespathways KEGG
updated 2.6 years ago by ★ 4.0k • written 2.6 years ago by • 0
0
votes
1
reply
1.1k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
votes
1
reply
1.6k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.9 years ago by ★ 4.0k • written 2.9 years ago by • 0
0
votes
0
replies
1.0k
views
Editing KEGG pathways in R
KEGG
3.2 years ago Jordan • 0
1
vote
0
replies
1.7k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
3.2 years ago makrez ▴ 10
1
vote
0
replies
1.6k
views
documentation on clusterProfiler output
clusterProfiler KEGG
3.2 years ago rafaela.perez ▴ 10
0
votes
6
replies
4.5k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.4 years ago Bogdan ▴ 670
0
votes
2
replies
2.4k
views
Drawing custom KEGG pathways
pathview KEGG
3.6 years ago curiousmind007 ▴ 10
0
votes
2
replies
2.5k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.6 years ago by 67k • written 3.6 years ago by • 0
0
votes
0
replies
1.3k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.8 years ago jol.espinoz ▴ 40
6
votes
5
replies
1.9k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.8 years ago by ★ 1.6k • written 3.8 years ago by • 0
2
votes
2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.1 years ago by 67k • written 4.1 years ago by • 0
0
votes
3
replies
1.4k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.6 years ago by 67k • written 4.6 years ago by ▴ 670
0
votes
1
reply
2.2k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.7 years ago by 25k • written 4.7 years ago by • 0
2
votes
2
replies
1.5k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.8 years ago by 67k • written 4.8 years ago by ▴ 20
0
votes
0
replies
982
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.8 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
1.4k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 4.9 years ago by 52k • written 5.3 years ago by ▴ 50
50 results • Page 1 of 1
Recent ...
Replies
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
It is not possible to use both. estimateGLMRobustDisp() estimates negative binomial dispersions for each gene, whereas glmQLFit() estimates…
Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0
Thank you. What is the difference between setting robust=TRUE in glmQLFit and estimateGLMRobustDisp? The paper i mentioned in the post used…
Comment: PCA of different bacterial species by Jeremy • 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error? by Urotree • 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Comment: RnBeads::combine() - error? by Urotree • 0
![enter image description here][1] [1]: /media/images/40d9778d-b044-4405-9b3d-2ba835f6 Hi, after I convert to RnBiseqSet, it shows "All…
Votes
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis
scater/scran with TPMs from Salmon - counts?
A: Full length single-cell RNA-seq - tximport output for downstream analysis
Answer: Understanding tximport working with salmon outputs
Answer: enrichGOgradient color change
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