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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4.3k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 19 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
votes
5
replies
3.4k
views
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 7.9 years ago by ★ 1.2k • written 7.9 years ago by ▴ 20
1
vote
3
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3.1k
views
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
4.1 years ago felix.thaler • 0
3
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4
replies
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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2.3k
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ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.1 years ago juls • 0
2
votes
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
2.2k
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 4.5 years ago by 25k • written 4.5 years ago by • 0
0
votes
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
votes
5
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2.0k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.2 years ago thomasjenner333 • 0
0
votes
3
replies
1.9k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
0
votes
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 6.6 years ago by ▴ 150 • written 6.6 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
votes
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 4.1 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
votes
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
replies
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
963
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
951
views
ReactomePA and genelist
ReactomePA
updated 5.0 years ago by • 0 • written 5.1 years ago by ▴ 10
0
votes
0
replies
852
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.2 years ago Lluís Revilla Sancho ▴ 730
0
votes
0
replies
793
views
viewPathway not showing a gene of interest
ReactomePA
5.3 years ago santos22903 • 0
0
votes
0
replies
777
views
reactomePA error input file
r reactomePA enrichment
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
0
votes
0
replies
771
views
ReactomePA only showing 1 result
ReactomePA
5.0 years ago ayang • 0
1
vote
1
reply
638
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by ▴ 10
0
votes
0
replies
616
views
ReactomePA list of pathway plots
ReactomePA
23 months ago curiousmind007 ▴ 10
0
votes
0
replies
570
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
3.5 years ago paun_bio • 0
40 results • Page 1 of 1
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Marcel Ramos 690
`BiocManager` does not install local packages. It only installs Bioconductor, CRAN, and GitHub ones. You should install local packages w…
Comment: error running enricher from clusterprofiler by Yael • 0
It worked!!! Thanks alot, i think something in the gene_list wasnt right... Thanks agian
Comment: Create protein sequences including variants from a VCF file by Yun • 0
This cannot work for a SNV file, since `injectSNPs` need a `SNPlocs` object
Comment: Can log2cpm be used for proteomics data normalization? by Daniel • 0
Thank you for the quick reply and I apologize for it being on the wrong thread but the "post tag" function wasn't working properly.
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db") by Patadù ▴ 10
I have arranged the code again following the other post and also the script you suggested. Now, I managed to install `org.Vdahliae.eg.db`. …
Votes
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Answer: Trim/Filter out-of-bounds GRanges
Comment: How to correctly adjust for gender in edgeR
Create protein sequences including variants from a VCF file
A: DEXSeq design formula
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