Showing : kegg • reset
1
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3
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2.6k
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Regarding the issue of background genes in enrichment analysis
KEGG goTools seqTools
written 8 months ago by ▴ 10
0
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4
replies
3.5k
views
Drawing custom KEGG pathways
pathview KEGG
written 4.8 years ago by ▴ 10
0
votes
1
reply
894
views
KEGG GSEA using Clusterprofiler - ncbi-geneid missing?
clusterProfiler KEGG
13 months ago Jessica • 0
0
votes
2
replies
1.1k
views
How to visualize these pathways using pathview
Salmo_salar RNASeq KEGG pathview
13 months ago ingrid.h • 0
1
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4
replies
1.1k
views
pathview - multiple states
pathview Pathways KEGG
15 months ago Philippine • 0
1
vote
2
replies
1.2k
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 17 months ago by ▴ 60 • written 17 months ago by • 0
0
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0
replies
653
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
20 months ago cereyredondo • 0
0
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3
replies
1.3k
views
pathview error
KEGGgraph KEGG
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
0
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0
replies
575
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
22 months ago danalvoronov ▴ 10
1
vote
1
reply
861
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 22 months ago by 68k • written 22 months ago by ▴ 30
5
votes
13
replies
4.6k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
22 months ago fernanda.backsouza ▴ 30
4
votes
2
replies
1.0k
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 22 months ago by ★ 4.1k • written 23 months ago by ▴ 30
2
votes
4
replies
2.8k
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
written 23 months ago by • 0
2
votes
2
replies
840
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
0
votes
0
replies
986
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
2.4 years ago mch • 0
0
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4
replies
4.3k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 17 months ago by • 0 • written 2.5 years ago by • 0
3
votes
2
replies
3.6k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 2.6 years ago by ★ 4.1k • written 2.6 years ago by ▴ 10
0
votes
0
replies
906
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
2.6 years ago georgii.vdovin • 0
1
vote
4
replies
2.5k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
2.7 years ago Jiyoung Lee • 0
0
votes
1
reply
1.2k
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
0
votes
5
replies
3.1k
views
enrichKEGG function error
cluster clusterProfiler KEGG
2.9 years ago • updated 2.8 years ago ruba-mahmoud • 0
1
vote
3
replies
2.9k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 2.9 years ago by ★ 4.1k • written 2.9 years ago by ▴ 10
0
votes
13
replies
16k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
3.0 years ago Laia ▴ 10
0
votes
5
replies
2.5k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 3.0 years ago by • 0
4
votes
11
replies
6.1k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 2.8 years ago by • 0 • written 3.0 years ago by ▴ 10
4
votes
2
replies
7.6k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 3.0 years ago by ▴ 50 • written 3.0 years ago by • 0
1
vote
7
replies
5.2k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by ▴ 10
2
votes
6
replies
5.7k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 2.2 years ago by ★ 4.1k • written 3.0 years ago by ▴ 10
1
vote
3
replies
2.4k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 3.2 years ago by 68k • written 3.3 years ago by • 0
4
votes
2
replies
5.8k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
3.4 years ago Wuschel ▴ 10
0
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2
replies
1.3k
views
Shivani
kegg
updated 3.4 years ago by ▴ 60 • written 3.4 years ago by • 0
4
votes
6
replies
6.5k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 3.5 years ago by ★ 4.1k • written 3.7 years ago by ▴ 10
3
votes
13
replies
4.8k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.6 years ago • updated 3.1 years ago nute11a ▴ 10
0
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3
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1.7k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
3.6 years ago abf ▴ 30
1
vote
1
reply
2.1k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 20
0
votes
2
replies
1.6k
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 3.6 years ago by ▴ 70 • written 3.6 years ago by ▴ 20
1
vote
3
replies
3.5k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 2.1 years ago by • 0 • written 3.8 years ago by • 0
0
votes
2
replies
4.3k
views
KEGG Pathway in R
keggrespathways KEGG
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
votes
1
reply
1.5k
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
0
votes
1
reply
2.1k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
0
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0
replies
1.4k
views
Editing KEGG pathways in R
KEGG
4.4 years ago Jordan • 0
1
vote
0
replies
2.2k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
4.4 years ago makrez ▴ 10
1
vote
0
replies
2.4k
views
documentation on clusterProfiler output
clusterProfiler KEGG
4.4 years ago rafaela.perez ▴ 10
0
votes
6
replies
7.8k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
4.6 years ago Bogdan ▴ 670
0
votes
2
replies
3.0k
views
Can't install KEGGprofile
KEGG RNASeq
updated 4.8 years ago by 68k • written 4.8 years ago by • 0
0
votes
0
replies
1.8k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
5.0 years ago jol.espinoz ▴ 40
6
votes
5
replies
2.5k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 5.0 years ago by ★ 1.6k • written 5.0 years ago by • 0
2
votes
2
replies
1.7k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 5.3 years ago by 68k • written 5.3 years ago by • 0
0
votes
3
replies
1.9k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 5.8 years ago by 68k • written 5.8 years ago by ▴ 670
0
votes
1
reply
3.1k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 5.9 years ago by 25k • written 5.9 years ago by • 0
113 results • Page 1 of 3
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Replies
Comment: Convergence Issues and Model Selection DESeq2 by dani.guan.3 • 0
Hi Michael, Thank you for your quick response and suggestion. I tried the following to determine if Batch was necessary in my design: …
Comment: Quick two questions on limpa by J Kim • 0
Thank you very much for taking the time to offer your advice and comments. I truly appreciate them. Best regards, J Kim
Answer: Convergence Issues and Model Selection DESeq2 by Michael Love 43k
You could try `glmGamPoi` fitting via `fitType`: https://github.com/thelovelab/DESeq2/blob/devel/man/DESeq.Rd#L10 This is a more rece…
Answer: Quick two questions on limpa by Gordon Smyth 53k
Thanks for your questions about limpa. The short answer is that you should use the default settings of the readSpectronaut() function. The…
Comment: ComplexHeatmap removes row labels if annotation is added by RosaliaSchulist99 • 0
thanks for sharing https://jokergoo.github.io/ComplexHeatmap-reference/book/a-list-of-heatmaps.html#automatic-adjustment-to-the-main-heatmap
Votes
Answer: Quick two questions on limpa
Answer: Quick two questions on limpa
Comment: tximeta cannot open annotation gtf?
Answer: tximeta cannot open annotation gtf?
Comment: Question about using LRT test for time course experiments with DESeq2
Awards • All
Scholar to Gordon Smyth 53k
Popular Question to shepherl 4.3k
Popular Question to helucro ▴ 70
Teacher to ATpoint ★ 5.0k
Teacher to Michael Love 43k
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