Showing : reactomePA • reset
3
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Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
4
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4
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4.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 18 months ago by • 0 • written 7.7 years ago by ▴ 660
0
votes
1
reply
4.0k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 4.1 years ago by ★ 1.2k • written 4.1 years ago by ▴ 10
2
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5
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3.3k
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How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 5.4 years ago by ★ 1.2k • written 5.4 years ago by ▴ 30
0
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14
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3.3k
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Error in ReactomePA
r reactomepa
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by ▴ 20
1
vote
3
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3.0k
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Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 8.6 years ago by ▴ 10 • written 8.6 years ago by ▴ 10
0
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8
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2.5k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.0 years ago felix.thaler • 0
3
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4
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2.3k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.2 years ago florianjt • 0
1
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8
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2.2k
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ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.1 years ago juls • 0
2
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4
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2.2k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.0 years ago by ★ 1.2k • written 6.0 years ago by • 0
2
votes
4
replies
2.1k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 9.1 years ago by ★ 1.2k • written 9.1 years ago by ▴ 140
0
votes
2
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2.0k
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 4.4 years ago by 25k • written 4.4 years ago by • 0
0
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2
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2.0k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
3
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5
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2.0k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.1 years ago thomasjenner333 • 0
0
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3
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1.9k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
0
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5
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1.9k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
5.9 years ago martin.busch • 0
3
votes
4
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1.9k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 6.5 years ago by ▴ 150 • written 6.5 years ago by ▴ 10
0
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1
reply
1.8k
views
ReactomePA - Change colors in barplot
reactomepa
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by ▴ 860
5
votes
4
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1.8k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 7.3 years ago by ▴ 100 • written 7.3 years ago by ▴ 40
1
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2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.9 years ago martin.busch • 0
0
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9
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1.6k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
3.9 years ago camillab. ▴ 10
1
vote
1
reply
1.6k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.3 years ago Kajus Baidžajevas ▴ 10
0
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2
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1.6k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by • 0
1
vote
2
replies
1.6k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 17 months ago by ▴ 40 • written 4.0 years ago by ▴ 10
1
vote
1
reply
1.5k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 7.6 years ago by ★ 1.2k • written 7.6 years ago by ▴ 10
0
votes
1
reply
1.3k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
6.9 years ago bhgyu ▴ 30
0
votes
4
replies
1.3k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
0
votes
1
reply
1.3k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 2.3 years ago by 3.9k • written 2.3 years ago by ▴ 20
0
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1
reply
1.3k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 7.6 years ago by 65k • written 7.6 years ago by • 0
0
votes
2
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1.2k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 3.9 years ago by 65k • written 3.9 years ago by • 0
3
votes
1
reply
1.2k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 6.9 years ago by ▴ 730 • written 6.9 years ago by • 0
0
votes
0
replies
954
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
4.0 years ago jan.soderman • 0
0
votes
1
reply
941
views
ReactomePA and genelist
ReactomePA
updated 5.0 years ago by • 0 • written 5.0 years ago by ▴ 10
0
votes
0
replies
846
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.2 years ago Lluís Revilla Sancho ▴ 730
0
votes
0
replies
792
views
viewPathway not showing a gene of interest
ReactomePA
5.2 years ago santos22903 • 0
0
votes
0
replies
770
views
reactomePA error input file
r reactomePA enrichment
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
0
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0
replies
766
views
ReactomePA only showing 1 result
ReactomePA
4.9 years ago ayang • 0
1
vote
1
reply
633
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by ▴ 10
0
votes
0
replies
608
views
ReactomePA list of pathway plots
ReactomePA
23 months ago curiousmind007 ▴ 10
0
votes
0
replies
562
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
3.5 years ago paun_bio • 0
40 results • Page 1 of 1
Recent ...
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Comment: Too many significant genes when integrating gtex and tcga by ATpoint ★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result by ATpoint ★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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