Showing : Kegg • reset
1
vote
4
replies
342
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
672
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 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…
Comment: RnBeads::combine() - error? by Urotree • 0
rnb.set.biseq <- RnBiseqSet( pheno = pheno, sites = sites, meth = meth, covg = NULL, # This can be NULL if coverage …
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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