Showing : ReactomePA • reset
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Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 4 weeks ago by ▴ 300 • written 4 weeks ago by ▴ 10
0
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1
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276
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 4 months ago by 3.1k • written 4 months ago by ▴ 20
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0
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277
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enrichPathway error when checking condition lengths used
DOSE ReactomePA
15 months ago Lluís Revilla Sancho ▴ 660
3
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4
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512
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Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
15 months ago florianjt • 0
0
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0
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240
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Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
18 months ago paun_bio • 0
0
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2
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400
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Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 23 months ago by 59k • written 23 months ago by • 0
0
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9
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611
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ReactomePA error graph
r rnaseq bulk GO ReactomePA
23 months ago camillab. ▴ 10
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0
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333
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reactomePA error input file
r reactomePA enrichment
updated 24 months ago by 3.5k • written 24 months ago by ▴ 10
0
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0
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351
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similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
2.1 years ago jan.soderman • 0
1
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1
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464
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ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 2.1 years ago by 3.5k • written 2.1 years ago by • 0
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8
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1.0k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
2.1 years ago felix.thaler • 0
0
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1
reply
1.5k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 2.2 years ago by ★ 1.2k • written 2.2 years ago by ▴ 10
0
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4
replies
418
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 2.2 years ago by 59k • written 2.2 years ago by • 0
0
votes
2
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959
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 2.5 years ago by 25k • written 2.5 years ago by • 0
0
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0
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416
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ReactomePA only showing 1 result
ReactomePA
3.0 years ago ayang • 0
0
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1
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403
views
ReactomePA and genelist
ReactomePA
updated 3.0 years ago by • 0 • written 3.1 years ago by ▴ 10
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0
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404
views
viewPathway not showing a gene of interest
ReactomePA
3.3 years ago santos22903 • 0
2
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5
replies
1.7k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 3.4 years ago by ★ 1.2k • written 3.5 years ago by ▴ 20
1
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2
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1.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
3.9 years ago martin.busch • 0
0
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5
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968
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
4.0 years ago martin.busch • 0
2
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4
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1.1k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 4.0 years ago by ★ 1.2k • written 4.0 years ago by • 0
0
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2
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1.0k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 4.2 years ago by ★ 1.2k • written 4.2 years ago by • 0
3
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5
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1.0k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
4.2 years ago thomasjenner333 • 0
0
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2
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879
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 4.3 years ago by ★ 1.2k • written 4.3 years ago by • 0
0
votes
3
replies
1.0k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
4.4 years ago andrew.gehrke • 0
3
votes
2
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2.5k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 4.5 years ago by ★ 1.2k • written 4.5 years ago by ▴ 10
3
votes
4
replies
1.0k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 4.6 years ago by ▴ 150 • written 4.6 years ago by ▴ 10
3
votes
1
reply
686
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 4.9 years ago by ▴ 660 • written 4.9 years ago by • 0
0
votes
1
reply
819
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
5.0 years ago bhgyu ▴ 30
1
vote
8
replies
1.2k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
5.2 years ago juls • 0
1
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1
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1.0k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
5.4 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
1.1k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 5.4 years ago by ▴ 100 • written 5.4 years ago by ▴ 30
0
votes
1
reply
915
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 5.6 years ago by 59k • written 5.6 years ago by • 0
1
vote
1
reply
1.1k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 5.7 years ago by ★ 1.2k • written 5.7 years ago by ▴ 10
4
votes
3
replies
1.4k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 5.7 years ago by ★ 1.2k • written 5.7 years ago by ▴ 610
0
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1
reply
1.0k
views
ReactomePA - Change colors in barplot
reactomepa
updated 5.8 years ago by ★ 1.2k • written 5.8 years ago by ▴ 860
0
votes
14
replies
2.1k
views
Error in ReactomePA
r reactomepa
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by ▴ 20
1
vote
3
replies
1.8k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 6.6 years ago by ▴ 10 • written 6.6 years ago by ▴ 10
2
votes
4
replies
1.6k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by ▴ 140
39 results • Page 1 of 1
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Comment: broken chain import in liftOver by Marcel Ramos 570
You could also try using one of the chain files in `AnnotationHub`, which gets auto-cached: ```r library(AnnotationHub) query(ah <- Annot…
Answer: paired analysis : return data matrix with indvidual/subject effects eliminated. by James W. MacDonald 59k
See `removeBatchEffect` in the `limma` package.
Comment: GDCdownload Directory Problem :( by Marcel Ramos 570
FWIW, `TCGAutils` is not a related package.
Comment: help please！ by 1051444231 • 0
I have updated Rtools
Comment: help please！ by 1051444231 • 0
> BiocManager::install("AnnotationDbi",force = TRUE) 'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' …
Votes
Answer: broken chain import in liftOver
Answer: toGRanges help!
Answer: toGRanges help!
Comment: CPM after RUVseq
A: Using the plotting functions of clusterProfiler / enrichplot with enrichment res
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