Showing : reactomePA • reset
2
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
8 days ago • updated 7 days ago Yifeii.Ge • 0
1
vote
2
replies
1.8k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 23 months ago by ▴ 40 • written 4.5 years ago by ▴ 10
4
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4
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4.9k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.1 years ago by • 0 • written 8.2 years ago by ▴ 660
0
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0
replies
762
views
ReactomePA list of pathway plots
ReactomePA
2.4 years ago curiousmind007 ▴ 10
1
vote
1
reply
789
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by ▴ 10
0
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1
reply
1.6k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 2.8 years ago by 4.1k • written 2.8 years ago by ▴ 20
0
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0
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969
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.7 years ago Lluís Revilla Sancho ▴ 760
3
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4
replies
2.8k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.7 years ago florianjt • 0
0
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0
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690
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.0 years ago paun_bio • 0
0
votes
2
replies
1.5k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
0
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9
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1.9k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.4 years ago camillab. ▴ 10
0
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0
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917
views
reactomePA error input file
r reactomePA enrichment
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by ▴ 10
0
votes
0
replies
1.1k
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
4.5 years ago jan.soderman • 0
0
votes
8
replies
2.9k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.6 years ago felix.thaler • 0
0
votes
1
reply
4.5k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 4.6 years ago by ★ 1.2k • written 4.6 years ago by ▴ 10
0
votes
4
replies
1.9k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
0
votes
2
replies
2.3k
views
DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
software error reactomePA DOSE DO.db there is no package called ‘DO.db’
updated 4.9 years ago by 25k • written 4.9 years ago by • 0
0
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0
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873
views
ReactomePA only showing 1 result
ReactomePA
5.4 years ago ayang • 0
0
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1
reply
1.1k
views
ReactomePA and genelist
ReactomePA
updated 5.5 years ago by • 0 • written 5.5 years ago by ▴ 10
0
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0
replies
884
views
viewPathway not showing a gene of interest
ReactomePA
5.8 years ago santos22903 • 0
2
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5
replies
3.9k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by ▴ 30
1
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2
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2.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.4 years ago martin.busch • 0
0
votes
5
replies
2.2k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
6.4 years ago martin.busch • 0
2
votes
4
replies
2.5k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by • 0
0
votes
2
replies
2.3k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 6.6 years ago by ★ 1.2k • written 6.6 years ago by • 0
3
votes
5
replies
2.3k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.7 years ago thomasjenner333 • 0
0
votes
2
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1.8k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
0
votes
3
replies
2.2k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.8 years ago andrew.gehrke • 0
3
votes
2
replies
5.7k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by ▴ 10
3
votes
4
replies
2.1k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 7.0 years ago by ▴ 150 • written 7.0 years ago by ▴ 10
3
votes
1
reply
1.3k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 7.4 years ago by ▴ 760 • written 7.4 years ago by • 0
0
votes
1
reply
1.5k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
7.4 years ago bhgyu ▴ 30
1
vote
8
replies
2.5k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.6 years ago juls • 0
1
vote
1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.8 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
2.0k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 7.8 years ago by ▴ 100 • written 7.8 years ago by ▴ 40
0
votes
1
reply
1.4k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 8.1 years ago by 67k • written 8.1 years ago by • 0
1
vote
1
reply
1.7k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 8.1 years ago by ★ 1.2k • written 8.1 years ago by ▴ 10
0
votes
1
reply
2.1k
views
ReactomePA - Change colors in barplot
reactomepa
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 860
0
votes
14
replies
3.7k
views
Error in ReactomePA
r reactomepa
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by ▴ 20
1
vote
3
replies
3.5k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 9.1 years ago by ▴ 10 • written 9.1 years ago by ▴ 10
2
votes
4
replies
2.4k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 9.6 years ago by ★ 1.2k • written 9.6 years ago by ▴ 140
41 results • Page 1 of 1
Recent ...
Replies
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Fahd • 0
Thanks for looking into this. This issue results in the incorrect usage of multiple ORA software including EnrichR.
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
Yes, I understand the implications of replacing the `OrgDb` packages in release. Maybe an upload to the annotationHub or GitHub could be an…
Votes
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
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