Showing : reactomepa • reset
2
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
4 months ago Yifeii.Ge • 0
1
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2
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2.0k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 2.3 years ago by ▴ 40 • written 4.9 years ago by ▴ 10
4
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4
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5.4k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.4 years ago by • 0 • written 8.5 years ago by ▴ 680
0
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0
replies
854
views
ReactomePA list of pathway plots
ReactomePA
2.8 years ago curiousmind007 ▴ 10
1
vote
1
reply
872
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by ▴ 10
0
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1
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1.7k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 3.2 years ago by 4.1k • written 3.2 years ago by ▴ 20
0
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0
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1.0k
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
4.1 years ago Lluís Revilla Sancho ▴ 760
3
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4
replies
3.1k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
4.1 years ago florianjt • 0
0
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0
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751
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.3 years ago paun_bio • 0
0
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2
replies
1.6k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
0
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9
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2.1k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.7 years ago camillab. ▴ 10
0
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0
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996
views
reactomePA error input file
r reactomePA enrichment
updated 4.8 years ago by ★ 4.0k • written 4.8 years ago by ▴ 10
0
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0
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1.2k
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
4.9 years ago jan.soderman • 0
0
votes
8
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3.1k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.9 years ago felix.thaler • 0
0
votes
1
reply
4.9k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 5.0 years ago by ★ 1.2k • written 5.0 years ago by ▴ 10
0
votes
4
replies
2.5k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
votes
2
replies
2.5k
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 5.3 years ago by 25k • written 5.3 years ago by • 0
0
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0
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929
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ReactomePA only showing 1 result
ReactomePA
5.8 years ago ayang • 0
0
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1
reply
1.3k
views
ReactomePA and genelist
ReactomePA
updated 5.8 years ago by • 0 • written 5.9 years ago by ▴ 10
0
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0
replies
953
views
viewPathway not showing a gene of interest
ReactomePA
6.1 years ago santos22903 • 0
2
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5
replies
4.2k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 6.2 years ago by ★ 1.2k • written 6.3 years ago by ▴ 30
1
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2
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2.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.7 years ago martin.busch • 0
0
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5
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2.4k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
6.8 years ago martin.busch • 0
2
votes
4
replies
2.8k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
0
votes
2
replies
2.5k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by • 0
3
votes
5
replies
2.5k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
7.0 years ago thomasjenner333 • 0
0
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2
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1.9k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by • 0
0
votes
3
replies
2.4k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
7.2 years ago andrew.gehrke • 0
3
votes
2
replies
6.4k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.3 years ago by ★ 1.2k • written 7.3 years ago by ▴ 10
3
votes
4
replies
2.4k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 7.4 years ago by ▴ 150 • written 7.4 years ago by ▴ 10
3
votes
1
reply
1.4k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 7.7 years ago by ▴ 760 • written 7.7 years ago by • 0
0
votes
1
reply
1.6k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
7.8 years ago bhgyu ▴ 30
1
vote
8
replies
2.7k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
8.0 years ago juls • 0
1
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1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
8.2 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
2.2k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 8.2 years ago by ▴ 100 • written 8.2 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
1
vote
1
reply
1.7k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 8.5 years ago by ★ 1.2k • written 8.5 years ago by ▴ 10
0
votes
1
reply
2.2k
views
ReactomePA - Change colors in barplot
reactomepa
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by ▴ 860
0
votes
14
replies
4.0k
views
Error in ReactomePA
r reactomepa
updated 8.7 years ago by ★ 1.2k • written 8.7 years ago by ▴ 20
1
vote
3
replies
3.8k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 9.4 years ago by ▴ 10 • written 9.4 years ago by ▴ 10
2
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4
replies
2.5k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 10.0 years ago by ★ 1.2k • written 10.0 years ago by ▴ 140
41 results • Page 1 of 1
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Comment: DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) by aitor • 0
Hi everyone. I have a RIP-Seq analysis with 3 conditions and 3 assays (IP, IgG and Input for each of them). 4 replicates for each conditio…
Comment: Discrepancy between Excel TPP-TR reported values and the Melt Curve reported val by James W. MacDonald 68k
You will need to provide a self-contained example, or it is unlikely that anybody could debug any possible issue.
Answer: Limma - Complex 2-way multi-level contrast with paired samples by James W. MacDonald 68k
If you are fitting donor as a fixed effect you do not also need to fit as a random effect. The limma package fits a generalized least squar…
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by ATpoint ★ 4.7k
Yes, perfectly valid. Analyzing counts from high-throughput experiments with DESeq2 (or edgeR, or limma) is standard. After all, what DiffB…
Comment: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf by AB ▴ 110
Force=TRUE did the trick. Thank you.
Votes
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
Answer: Differential expression of proteins using somascan data
Answer: Surprising behavior for DEXseq dispersion estimate plot?
Answer: Handle zero effective gene length when tximport RSEM results
Handle zero effective gene length when tximport RSEM results
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