Showing : KEGG • reset
0
votes
3
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117
views
pathview error
KEGGgraph KEGG
updated 3 days ago by ★ 4.0k • written 4 days ago by • 0
0
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0
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74
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
10 days ago danalvoronov ▴ 10
2
votes
13
replies
556
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
5 weeks ago • updated 4 weeks ago fernanda.backsouza ▴ 10
1
vote
1
reply
143
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 4 weeks ago by 66k • written 4 weeks ago by ▴ 10
3
votes
2
replies
251
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 4 weeks ago by ★ 4.0k • written 5 weeks ago by ▴ 10
2
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2
replies
228
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
6 weeks ago julia_mcdonough • 0
2
votes
2
replies
283
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
1
vote
3
replies
1.9k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 3 months 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 ★ 4.0k • written 15 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
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0
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378
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
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5
replies
1.3k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 14 months ago by • 0
0
votes
3
replies
1.3k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 7 months ago by ▴ 20 • written 8 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 ★ 4.0k • written 9 months ago by ▴ 10
0
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0
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368
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
10 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 Jiyoung Lee • 0
0
votes
1
reply
580
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 11 months ago by 42k • written 12 months ago by • 0
4
votes
11
replies
2.7k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 12 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 5.6 years ago by • 0
0
votes
5
replies
1.4k
views
enrichKEGG function error
cluster clusterProfiler KEGG
13 months ago • updated 12 months ago ruba-mahmoud • 0
1
vote
3
replies
1.2k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 13 months ago by ★ 4.0k • written 13 months ago by ▴ 10
0
votes
13
replies
5.1k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
14 months ago Laia ▴ 10
1
vote
7
replies
1.9k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 15 months ago by ▴ 780 • written 15 months ago by ▴ 10
4
votes
2
replies
4.6k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 15 months ago by ▴ 50 • written 15 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 17 months ago by 66k • written 18 months ago by • 0
4
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2
replies
2.0k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
19 months ago Wuschel ▴ 10
0
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2
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714
views
Shivani
kegg
updated 19 months ago by ▴ 40 • written 19 months ago by • 0
4
votes
6
replies
3.7k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 21 months ago by ★ 4.0k • written 23 months ago by ▴ 10
0
votes
3
replies
976
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
22 months ago • updated 21 months ago abf ▴ 30
1
vote
1
reply
1.2k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 22 months ago by 66k • written 22 months ago by ▴ 20
0
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2
replies
881
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 22 months ago by ▴ 70 • written 22 months ago by ▴ 20
0
votes
2
replies
3.3k
views
KEGG Pathway in R
keggrespathways KEGG
updated 24 months ago by ★ 3.9k • written 24 months ago by • 0
0
votes
1
reply
857
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
1.3k
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
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0
replies
831
views
Editing KEGG pathways in R
KEGG
2.6 years ago Jordan • 0
1
vote
0
replies
1.4k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.6 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
3.8k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
2.8 years ago Bogdan ▴ 670
2
votes
3
replies
4.9k
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 2.9 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 curiousmind007 ▴ 10
0
votes
2
replies
2.2k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.0 years ago by 66k • 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
3.2 years ago jol.espinoz ▴ 40
6
votes
5
replies
1.6k
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
1.2k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.5 years ago by 66k • written 3.5 years ago by • 0
0
votes
3
replies
1.1k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.0 years ago by 66k • written 4.0 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 4.2 years ago by 66k • written 4.2 years ago by ▴ 10
0
votes
0
replies
796
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.2 years ago Assa Yeroslaviz ★ 1.5k
50 results • Page 1 of 1
Recent ...
Replies
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30
I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…
Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k
My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …
Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Votes
A: Analyzing data without replicates using DiffBind
A: Analyzing data without replicates using DiffBind
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
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