Showing : Kegg • reset
0
votes
2
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220
views
Student
metaboliteIDmapping Metabolomics KEGG
updated 15 days ago by ▴ 60 • written 16 days ago by • 0
0
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0
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236
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
11 weeks ago cereyredondo • 0
0
votes
3
replies
454
views
pathview error
KEGGgraph KEGG
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
0
votes
0
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195
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
4 months ago danalvoronov ▴ 10
1
vote
1
reply
305
views
Cannabis OrgDb
KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware
updated 5 months ago by 67k • written 5 months ago by ▴ 20
4
votes
13
replies
1.6k
views
Trying to use enrichGO
clusterProfiler GenomicDistributionsData KEGG
5 months ago fernanda.backsouza ▴ 20
4
votes
2
replies
447
views
Cannabis and KEGGgraph
KEGGREST GenomicDistributionsData KEGGgraph KEGG
updated 5 months ago by ★ 4.1k • written 5 months ago by ▴ 20
2
votes
2
replies
557
views
How many of my genes from my gene list are in each KEGG pathway?
Pathways clusterProfiler gseKEGG KEGG
5 months ago julia_mcdonough • 0
2
votes
2
replies
433
views
Error in enrichKEGG for a model organism
enrichKEGG KEGGgraph KEGG
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
0
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0
replies
512
views
Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
11 months ago mch • 0
0
votes
3
replies
2.0k
views
pathview error "negative length vectors are not allowed
pathview kegg KEGG
updated 12 months ago by ▴ 30 • written 12 months ago by • 0
3
votes
2
replies
1.6k
views
ERROR in EnrichKEGG(), 'species should be listed' in, download method do not change
KEGG DESeq2 biomaRt clusterProfiler org.Mm.eg.db
updated 13 months ago by ★ 4.1k • written 13 months ago by ▴ 10
0
votes
0
replies
492
views
Downstream analysis of DEG for non-model organisms.
axolotl KEGG GOstats clusterProfiler
14 months ago georgii.vdovin • 0
1
vote
4
replies
1.4k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview KEGG Oryza_sativa
15 months ago Jiyoung Lee • 0
0
votes
1
reply
703
views
DESeq2 + analysis question for design with uneven time point design
timecourse KEGG DESeq2
updated 16 months ago by 42k • written 16 months ago by • 0
0
votes
5
replies
1.8k
views
enrichKEGG function error
cluster clusterProfiler KEGG
17 months ago ruba-mahmoud • 0
1
vote
3
replies
1.5k
views
how to add an enrichment score to a kegg pathway enrichment analysis?
KEGG clusterProfiler Bioconductor
updated 18 months ago by ★ 4.1k • written 18 months ago by ▴ 10
0
votes
13
replies
6.8k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
18 months ago Laia ▴ 10
0
votes
5
replies
1.6k
views
[limma::kegga] Pathway names all NA
KEGG limma
written 18 months ago by • 0
4
votes
11
replies
3.4k
views
Sudden error with KEGG analysis using gometh
KEGG gometh
updated 16 months ago by • 0 • written 19 months ago by ▴ 10
4
votes
2
replies
5.3k
views
gseKEGG - no gene can be mapped (RNAseq analysis)
KEGG clusterProfiler
updated 19 months ago by ▴ 50 • written 19 months ago by • 0
1
vote
7
replies
2.5k
views
Problem with universe argument in enrichKEGG
KEGG clusterProfiler keggorthology
updated 19 months ago by ▴ 780 • written 19 months ago by ▴ 10
2
votes
6
replies
2.7k
views
clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis
KEGG clusterProfiler
updated 9 months ago by ★ 4.1k • written 19 months ago by ▴ 10
1
vote
3
replies
1.4k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG TAIR_IDs KEGGdzPathwaysGEO pathview
updated 21 months ago by 67k • written 22 months ago by • 0
4
votes
2
replies
2.9k
views
Is there any description available for KEGG Pathway Edge Types
KEGG SystemsBiology KEGGgraph ontology
23 months ago Wuschel ▴ 10
0
votes
2
replies
858
views
Shivani
kegg
updated 23 months ago by ▴ 60 • written 23 months ago by • 0
4
votes
6
replies
4.3k
views
Pathview unable to download pathways
clusterProfiler KEGGgraph clusterpr KEGG pathview
updated 2.1 years ago by ★ 4.1k • written 2.3 years ago by ▴ 10
3
votes
13
replies
3.0k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.1 years ago • updated 20 months ago nute11a ▴ 10
0
votes
3
replies
1.2k
views
ROntoTools: Set returned by keggPathwayGraphs is missing 121 pathways reported by keggPathwayNames
KEGGREST ROntoTools KEGG KEGGgraph
2.2 years ago abf ▴ 30
1
vote
1
reply
1.4k
views
From KEGG ID's (Kxxxxx) to Uniprot IDs
KEGG UniProt.ws
updated 2.2 years ago by 67k • written 2.2 years ago by ▴ 20
0
votes
2
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1.0k
views
How do we get genes involved in all immune system pathways?
keggorthology KEGG
updated 2.2 years ago by ▴ 70 • written 2.2 years ago by ▴ 20
1
vote
3
replies
2.3k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 7 months ago by • 0 • written 2.3 years ago by • 0
0
votes
2
replies
3.6k
views
KEGG Pathway in R
keggrespathways KEGG
updated 2.3 years ago by ★ 4.0k • written 2.3 years ago by • 0
0
votes
1
reply
987
views
Tool for metagenomic functional analysis with 4-factor study design
Metagenomics DESeq2 metagenomeSeq edgeR KEGG
updated 2.5 years ago by 42k • written 2.5 years ago by • 0
0
votes
1
reply
1.4k
views
How to do functional analysis on differentially expressed gene list from RNA-seq data?
RNA-sequencing KEGG GO
updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by • 0
0
votes
0
replies
945
views
Editing KEGG pathways in R
KEGG
2.9 years ago Jordan • 0
1
vote
0
replies
1.5k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.9 years ago makrez ▴ 10
1
vote
0
replies
1.4k
views
documentation on clusterProfiler output
clusterProfiler KEGG
3.0 years ago rafaela.perez ▴ 10
0
votes
6
replies
4.2k
views
extracting the KEGG pathway for a set of genes
Pathways KEGG
3.2 years ago Bogdan ▴ 670
0
votes
2
replies
2.2k
views
Drawing custom KEGG pathways
pathview KEGG
3.4 years ago • updated 3.3 years ago curiousmind007 ▴ 10
0
votes
2
replies
2.4k
views
Can't install KEGGprofile
KEGG RNASeq
updated 3.4 years ago by 67k • written 3.4 years ago by • 0
0
votes
0
replies
1.2k
views
How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
KEGG KEGGREST keggorthology Metagenomics
3.5 years ago jol.espinoz ▴ 40
6
votes
5
replies
1.8k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.6 years ago by ★ 1.6k • written 3.6 years ago by • 0
2
votes
2
replies
1.3k
views
Pathway analysis and GO terms analysis with goseq
KEGG Pathways GO goseq
updated 3.8 years ago by 67k • written 3.8 years ago by • 0
0
votes
3
replies
1.3k
views
extracting the genes associated with a specific pathway
pathway KEGG annotation annotationhub
updated 4.3 years ago by 67k • written 4.3 years ago by ▴ 670
0
votes
1
reply
2.0k
views
KEGGREST keggGet fails to retrieve modules, but not pathways
keggrest software error pathways modules kegg
updated 4.5 years ago by 25k • written 4.5 years ago by • 0
2
votes
2
replies
1.4k
views
Specific KEGG.db pathways not found in KEGG.db package
KEGG.db KEGG KEGGPATHNAME2ID KEGGPATHID2EXTIT
updated 4.5 years ago by 67k • written 4.5 years ago by ▴ 20
0
votes
0
replies
932
views
plotting Signalling Pathways using SPIA
SPIA functional-analysis Pathways KEGG
4.5 years ago Assa Yeroslaviz ★ 1.5k
3
votes
1
reply
1.3k
views
Query relating pathway enrichment analysis for DEGs using KEGG or any other database.
KEGG R offline Pathway Enrichment
updated 4.6 years ago by 51k • written 5.0 years ago by ▴ 50
6
votes
6
replies
5.4k
views
Finding enriched pathways from a gene list.
microarray limma kegg ENTREZ enrichment analysis
updated 4.6 years ago by 51k • written 4.6 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: miRTarRnaseq library by mercedeh.movassagh ▴ 20
Hi Maria, so what is the code you are using? By the 3rd way to conduct the analysis do you mean looking at the interaction model from part …
Comment: miRTarRnaseq library by María Calvo • 0
Hello, in line with the previous questions, when the miRNA-mRNA interaction analysis is performed (3 rd way to conduct the analysis), I obt…
Answer: heatmap with batch effect by James W. MacDonald 67k
You have only one condition in the second batch, so it's not possible to remove the batch effect. You can probably adjust for it somewhat, …
Answer: how do I convert an Ilumn IDREF to a CPG loci by James W. MacDonald 67k
``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame with 865859 rows and 3 columns ch…
Answer: Which input data is acceptable for MAST? by Andrew_McDavid ▴ 270
Not too familiar with SCT v2. If it also has a point-mass at zero and the non-zero component is roughly-symmetric, then it might work ok w…
Votes
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Answer: How to control batch effect if Group and batch are same?
Comment: Convert HGVS Representation back to Reference Genome Coordinates
Answer: How to control batch effect if Group and batch are same?
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