Showing : ReactomePA • reset
5
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4
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Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 6.4 years ago by ▴ 100 • written 6.4 years ago by ▴ 30
4
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4
replies
2.7k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 7 months ago by • 0 • written 6.8 years ago by ▴ 660
3
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4
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1.4k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
2.3 years ago florianjt • 0
3
votes
4
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1.3k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 5.6 years ago by ▴ 150 • written 5.6 years ago by ▴ 10
3
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1
reply
923
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 5.9 years ago by ▴ 710 • written 5.9 years ago by • 0
3
votes
2
replies
3.5k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 5.6 years ago by ★ 1.2k • written 5.6 years ago by ▴ 10
3
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5
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1.4k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
5.2 years ago thomasjenner333 • 0
2
votes
4
replies
1.8k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 140
2
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5
replies
2.5k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 4.5 years ago by ★ 1.2k • written 4.5 years ago by ▴ 20
2
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4
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1.5k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 5.0 years ago by ★ 1.2k • written 5.0 years ago by • 0
1
vote
1
reply
1.3k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
6.4 years ago Kajus Baidžajevas ▴ 10
1
vote
3
replies
2.3k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 7.6 years ago by ▴ 10 • written 7.6 years ago by ▴ 10
1
vote
1
reply
1.3k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by ▴ 10
1
vote
2
replies
1.1k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 6 months ago by ▴ 40 • written 3.1 years ago by ▴ 10
1
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2
replies
1.4k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.0 years ago martin.busch • 0
1
vote
1
reply
343
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 13 months ago by ▴ 720 • written 13 months ago by ▴ 10
1
vote
8
replies
1.7k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
6.2 years ago juls • 0
0
votes
0
replies
605
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
3.1 years ago jan.soderman • 0
0
votes
0
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523
views
reactomePA error input file
r reactomePA enrichment
updated 3.0 years ago by 3.8k • written 3.0 years ago by ▴ 10
0
votes
2
replies
744
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 2.9 years ago by 63k • written 2.9 years ago by • 0
0
votes
0
replies
402
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
2.5 years ago paun_bio • 0
0
votes
0
replies
550
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
2.3 years ago Lluís Revilla Sancho ▴ 710
0
votes
1
reply
764
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 16 months ago by 3.5k • written 16 months ago by ▴ 20
0
votes
0
replies
278
views
ReactomePA list of pathway plots
ReactomePA
12 months ago curiousmind007 ▴ 10
0
votes
0
replies
572
views
ReactomePA only showing 1 result
ReactomePA
4.0 years ago ayang • 0
0
votes
14
replies
2.7k
views
Error in ReactomePA
r reactomepa
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by ▴ 20
0
votes
1
reply
1.4k
views
ReactomePA - Change colors in barplot
reactomepa
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by ▴ 860
0
votes
1
reply
1.1k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 6.7 years ago by 63k • written 6.7 years ago by • 0
0
votes
1
reply
1.0k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
6.0 years ago bhgyu ▴ 30
0
votes
3
replies
1.4k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
5.4 years ago andrew.gehrke • 0
0
votes
2
replies
1.2k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 5.3 years ago by ★ 1.2k • written 5.3 years ago by • 0
0
votes
2
replies
1.4k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 5.2 years ago by ★ 1.2k • written 5.2 years ago by • 0
0
votes
5
replies
1.4k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
5.0 years ago martin.busch • 0
0
votes
0
replies
593
views
viewPathway not showing a gene of interest
ReactomePA
4.3 years ago santos22903 • 0
0
votes
1
reply
586
views
ReactomePA and genelist
ReactomePA
updated 4.1 years ago by • 0 • written 4.1 years ago by ▴ 10
0
votes
2
replies
1.5k
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 3.5 years ago by 25k • written 3.5 years ago by • 0
0
votes
4
replies
664
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 3.3 years ago by 63k • written 3.3 years ago by • 0
0
votes
1
reply
3.0k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 3.2 years ago by ★ 1.2k • written 3.2 years ago by ▴ 10
0
votes
9
replies
979
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
2.9 years ago camillab. ▴ 10
0
votes
8
replies
1.8k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
3.1 years ago felix.thaler • 0
40 results • Page 1 of 1
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Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
Sure, noted.
Comment: Question on constructing design matrix and defining contrasts for analysis by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, I realized while re-running through the WGCNA workflow and forget to account for the paired experiment. For general gene …
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
PS. Just as aside, using `dput` to show a data.frame is unnecessary overkill. Just typing `targetsframe` at the prompt would do the job.
Comment: Question on constructing design matrix and defining contrasts for analysis by Gordon Smyth 47k
> Basically, I want to create a design matrix and binarize by 0 and 1 to be used in WGCNA analysis to compare module between/within groups …
Comment: SummarizedExperiment is now warning on attach about `read_block` namespace confl by ansleyharralson • 0
Any estimate on when DelayedArray 0.26.3 will be released for macOS Binary (arm64)? Latest is still 0.26.02 best I can tell.
Votes
WGCNA coupled with differential expression analysis: question about baseline module detection
WGCNA with paired samples
Comment: Question on constructing design matrix and defining contrasts for analysis
Comment: Question on constructing design matrix and defining contrasts for analysis
Answer: Question on constructing design matrix and defining contrasts for analysis
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