Showing : KEGG • reset
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KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
7 days ago Jessica • 0
0
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2
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499
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
21 days ago • updated 5 days ago ingrid.h • 0
1
vote
4
replies
455
views
pathview - multiple states
pathview Pathways KEGG
11 weeks ago • updated 10 weeks ago Philippine • 0
1
vote
2
replies
414
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 5 months ago by ▴ 60 • written 5 months ago by • 0
0
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0
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364
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How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
7 months ago cereyredondo • 0
0
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3
replies
798
views
pathview error
KEGGgraph KEGG
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
0
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0
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296
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
9 months ago danalvoronov ▴ 10
1
vote
1
reply
437
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 10 months ago by 68k • written 10 months ago by ▴ 30
5
votes
13
replies
2.6k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
10 months ago fernanda.backsouza ▴ 30
4
votes
2
replies
601
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 10 months ago by ★ 4.1k • written 10 months ago by ▴ 30
2
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3
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1.1k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
updated 3 months ago by • 0 • written 10 months ago by • 0
2
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2
replies
544
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
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0
replies
618
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
15 months ago mch • 0
0
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4
replies
2.8k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 4 months ago by • 0 • written 17 months ago by • 0
3
votes
2
replies
2.1k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 18 months ago by ★ 4.1k • written 18 months ago by ▴ 10
0
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0
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579
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
19 months ago georgii.vdovin • 0
1
vote
4
replies
1.7k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
20 months ago Jiyoung Lee • 0
0
votes
1
reply
813
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 20 months ago by 43k • written 21 months ago by • 0
0
votes
5
replies
2.2k
views
enrichKEGG function error
cluster clusterProfiler KEGG
22 months ago • updated 21 months ago ruba-mahmoud • 0
1
vote
3
replies
1.8k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 22 months ago by ★ 4.1k • written 22 months ago by ▴ 10
0
votes
13
replies
9.3k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
23 months ago Laia ▴ 10
0
votes
5
replies
1.9k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 23 months ago by • 0
4
votes
11
replies
4.1k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 21 months ago by • 0 • written 23 months ago by ▴ 10
4
votes
2
replies
6.2k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 23 months ago by ▴ 50 • written 24 months ago by • 0
1
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7
replies
3.0k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 23 months ago by ▴ 780 • written 24 months ago by ▴ 10
2
votes
6
replies
3.5k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 13 months ago by ★ 4.1k • written 24 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 2.2 years ago by 68k • written 2.2 years ago by • 0
4
votes
2
replies
3.7k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
2.3 years ago Wuschel ▴ 10
0
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2
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951
views
Shivani
kegg
updated 2.3 years ago by ▴ 60 • written 2.3 years ago by • 0
4
votes
6
replies
4.8k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.5 years ago by ★ 4.1k • written 2.7 years ago by ▴ 10
3
votes
13
replies
3.3k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.5 years ago • updated 2.0 years ago nute11a ▴ 10
0
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3
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1.3k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.5 years ago abf ▴ 30
1
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1
reply
1.6k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 2.5 years ago by 68k • written 2.5 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 2.6 years ago by ▴ 70 • written 2.6 years ago by ▴ 20
1
vote
3
replies
2.6k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 12 months ago by • 0 • written 2.7 years ago by • 0
0
votes
2
replies
3.9k
views
KEGG Pathway in R
keggrespathways KEGG
updated 2.7 years ago by ★ 4.0k • written 2.7 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 2.9 years ago by 43k • written 2.9 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 3.1 years ago by ★ 4.0k • written 3.1 years ago by • 0
0
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0
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1.1k
views
Editing KEGG pathways in R
KEGG
3.3 years ago Jordan • 0
1
vote
0
replies
1.8k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
3.3 years ago makrez ▴ 10
1
vote
0
replies
1.7k
views
documentation on clusterProfiler output
clusterProfiler KEGG
3.4 years ago rafaela.perez ▴ 10
0
votes
6
replies
4.9k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.5 years ago Bogdan ▴ 670
0
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2
replies
2.5k
views
Drawing custom KEGG pathways
pathview KEGG
3.8 years ago • updated 3.7 years ago curiousmind007 ▴ 10
0
votes
2
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2.6k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
0
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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
3.9 years ago jol.espinoz ▴ 40
6
votes
5
replies
1.9k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.9 years ago by ★ 1.6k • written 3.9 years ago by • 0
2
votes
2
replies
1.4k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 4.2 years ago by 68k • written 4.2 years ago by • 0
0
votes
3
replies
1.4k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.7 years ago by 68k • written 4.7 years ago by ▴ 670
0
votes
1
reply
2.3k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.9 years ago by 25k • written 4.9 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 4.9 years ago by 68k • written 4.9 years ago by ▴ 20
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Answer: Differential variance analysis - can i use deseq2 by Michael Love 43k
We don't have a test of differential variance but other Bioconductor packages can, check similar posts (even on the right side bar) or use …
Comment: For some reason I can't update BiocManager to 3.20 by shepherl 4.1k
It seems likely this was installed as an admin account and a user account would not be able to update. Someone with admin access should run…
Answer: UniProt.ws query for single UniRef90 ID takes several minutes by James W. MacDonald 68k
Any query over the internet can vary in the time to completion due to the vagaries of the connection you may have. I just tried your query …
Answer: batch effect removal for agilent microarray data by James W. MacDonald 68k
If all of the samples in group 155 are one type, and all the other samples in 438 are the other, then no. The biological and technical vari…
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Since `BiocManager::install` is a wrapper around `install.packages` you should be able to use the dependencies argument. Default is the de…
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Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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