Showing : reactomepa • reset
2
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
24 days ago Yifeii.Ge • 0
1
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2
replies
1.9k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 24 months ago by ▴ 40 • written 4.6 years ago by ▴ 10
4
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4
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5.0k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.1 years ago by • 0 • written 8.2 years ago by ▴ 660
0
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0
replies
770
views
ReactomePA list of pathway plots
ReactomePA
2.5 years ago curiousmind007 ▴ 10
1
vote
1
reply
800
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by ▴ 10
0
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1
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1.6k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 2.9 years ago by 4.1k • written 2.9 years ago by ▴ 20
0
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0
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973
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.8 years ago Lluís Revilla Sancho ▴ 760
3
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4
replies
2.8k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.8 years ago florianjt • 0
0
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0
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696
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.0 years ago paun_bio • 0
0
votes
2
replies
1.5k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 4.4 years ago by 67k • written 4.4 years ago by • 0
0
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9
replies
1.9k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.4 years ago camillab. ▴ 10
0
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0
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927
views
reactomePA error input file
r reactomePA enrichment
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 10
0
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0
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1.1k
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
4.6 years ago jan.soderman • 0
0
votes
8
replies
2.9k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.6 years ago felix.thaler • 0
0
votes
1
reply
4.5k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 4.7 years ago by ★ 1.2k • written 4.7 years ago by ▴ 10
0
votes
4
replies
2.0k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 4.7 years ago by 67k • written 4.7 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 5.0 years ago by 25k • written 5.0 years ago by • 0
0
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0
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876
views
ReactomePA only showing 1 result
ReactomePA
5.5 years ago ayang • 0
0
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1
reply
1.1k
views
ReactomePA and genelist
ReactomePA
updated 5.5 years ago by • 0 • written 5.6 years ago by ▴ 10
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0
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892
views
viewPathway not showing a gene of interest
ReactomePA
5.8 years ago santos22903 • 0
2
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5
replies
3.9k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 5.9 years ago by ★ 1.2k • written 6.0 years ago by ▴ 30
1
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2
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2.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.4 years ago martin.busch • 0
0
votes
5
replies
2.2k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
6.5 years ago martin.busch • 0
2
votes
4
replies
2.6k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by • 0
0
votes
2
replies
2.3k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by • 0
3
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5
replies
2.3k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.7 years ago thomasjenner333 • 0
0
votes
2
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1.8k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
0
votes
3
replies
2.3k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.9 years ago andrew.gehrke • 0
3
votes
2
replies
5.8k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by ▴ 10
3
votes
4
replies
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 7.1 years ago by ▴ 150 • written 7.1 years ago by ▴ 10
3
votes
1
reply
1.3k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 7.4 years ago by ▴ 760 • written 7.4 years ago by • 0
0
votes
1
reply
1.5k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
7.5 years ago bhgyu ▴ 30
1
vote
8
replies
2.6k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.7 years ago juls • 0
1
vote
1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.9 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
2.0k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 7.9 years ago by ▴ 100 • written 7.9 years ago by ▴ 40
0
votes
1
reply
1.4k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 8.1 years ago by 67k • written 8.1 years ago by • 0
1
vote
1
reply
1.7k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 10
0
votes
1
reply
2.1k
views
ReactomePA - Change colors in barplot
reactomepa
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by ▴ 860
0
votes
14
replies
3.8k
views
Error in ReactomePA
r reactomepa
updated 8.4 years ago by ★ 1.2k • written 8.4 years ago by ▴ 20
1
vote
3
replies
3.5k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 9.1 years ago by ▴ 10 • written 9.1 years ago by ▴ 10
2
votes
4
replies
2.4k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 9.7 years ago by ★ 1.2k • written 9.7 years ago by ▴ 140
41 results • Page 1 of 1
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Answer: ANOVA like approach of edgeR by Gordon Smyth 51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data by Gordon Smyth 51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Comment: Help with RSEM counts: do I transpose matrix? by NB • 0
Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?
Votes
Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom
Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (
Comment: does anyone how to create rarefaction curves from a phyloseq object?
Answer: ANOVA like approach of edgeR
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