Showing : ReactomePA • reset
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
12 weeks ago • updated 11 weeks ago Yifeii.Ge • 0
1
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2
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1.9k
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ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 2.1 years ago by ▴ 40 • written 4.7 years ago by ▴ 10
4
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4
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5.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.3 years ago by • 0 • written 8.4 years ago by ▴ 660
0
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0
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811
views
ReactomePA list of pathway plots
ReactomePA
2.6 years ago curiousmind007 ▴ 10
1
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1
reply
834
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.8 years ago by ▴ 780 • written 2.8 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 3.0 years ago by 4.1k • written 3.0 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
3.9 years ago Lluís Revilla Sancho ▴ 760
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4
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3.0k
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Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.9 years ago florianjt • 0
0
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0
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719
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Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.2 years ago paun_bio • 0
0
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2
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1.6k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 4.6 years ago by 67k • written 4.6 years ago by • 0
0
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9
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2.0k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.6 years ago camillab. ▴ 10
0
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0
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953
views
reactomePA error input file
r reactomePA enrichment
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 10
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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
4.7 years ago jan.soderman • 0
0
votes
8
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3.0k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.8 years ago felix.thaler • 0
0
votes
1
reply
4.7k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 4.8 years ago by ★ 1.2k • written 4.8 years ago by ▴ 10
0
votes
4
replies
2.2k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 4.9 years ago by 67k • written 4.9 years ago by • 0
0
votes
2
replies
2.4k
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 5.1 years ago by 25k • written 5.1 years ago by • 0
0
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0
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901
views
ReactomePA only showing 1 result
ReactomePA
5.7 years ago ayang • 0
0
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1
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1.2k
views
ReactomePA and genelist
ReactomePA
updated 5.7 years ago by • 0 • written 5.7 years ago by ▴ 10
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0
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921
views
viewPathway not showing a gene of interest
ReactomePA
6.0 years ago santos22903 • 0
2
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5
replies
4.1k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 6.1 years ago by ★ 1.2k • written 6.1 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
6.6 years ago martin.busch • 0
0
votes
5
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2.3k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
6.6 years ago martin.busch • 0
2
votes
4
replies
2.7k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by • 0
0
votes
2
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2.4k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
3
votes
5
replies
2.4k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.9 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 7.0 years ago by ★ 1.2k • written 7.0 years ago by • 0
0
votes
3
replies
2.3k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
7.0 years ago andrew.gehrke • 0
3
votes
2
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6.1k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by ▴ 10
3
votes
4
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2.2k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ▴ 10
3
votes
1
reply
1.4k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 7.6 years ago by ▴ 760 • written 7.6 years ago by • 0
0
votes
1
reply
1.5k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
7.6 years ago bhgyu ▴ 30
1
vote
8
replies
2.6k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.8 years ago juls • 0
1
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1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
8.0 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
2.1k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 8.0 years ago by ▴ 100 • written 8.0 years ago by ▴ 40
0
votes
1
reply
1.4k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 8.3 years ago by 67k • written 8.3 years ago by • 0
1
vote
1
reply
1.7k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by ▴ 10
0
votes
1
reply
2.1k
views
ReactomePA - Change colors in barplot
reactomepa
updated 8.4 years ago by ★ 1.2k • written 8.4 years ago by ▴ 860
0
votes
14
replies
3.9k
views
Error in ReactomePA
r reactomepa
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by ▴ 20
1
vote
3
replies
3.7k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 9.3 years ago by ▴ 10 • written 9.3 years ago by ▴ 10
2
votes
4
replies
2.5k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 9.8 years ago by ★ 1.2k • written 9.8 years ago by ▴ 140
41 results • Page 1 of 1
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Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Michael, Thank you very much!
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
Yes, with the knowledge that, it is expected to be underpowered.
Comment: Is there a way to do DEG analysis across two batches sharing one sample only? by georgeyu703 • 0
Thank you, Michael. How? Could you provide more details? Can I just do it as usual, I mean to include batch in the model?
Answer: Is there a way to do DEG analysis across two batches sharing one sample only? by Michael Love 43k
The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confounde…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA? by alserg ▴ 280
`NES > 0` means that your gene set has more genes with positive logFC/stat. In your case these genes should be up in Subset1. However, if y…
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Answer: Error in download.file for TCGAutils::symbolsToRanges
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