Showing : reactomePA • reset
5
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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
4
votes
4
replies
4.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 18 months ago by • 0 • written 7.6 years ago by ▴ 660
3
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4
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2.3k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.2 years ago florianjt • 0
3
votes
4
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1.8k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 6.5 years ago by ▴ 150 • written 6.5 years ago by ▴ 10
3
votes
1
reply
1.2k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 6.8 years ago by ▴ 730 • written 6.8 years ago by • 0
3
votes
2
replies
4.7k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 6.4 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
3
votes
5
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1.9k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.1 years ago thomasjenner333 • 0
2
votes
4
replies
2.1k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 9.1 years ago by ★ 1.2k • written 9.1 years ago by ▴ 140
2
votes
5
replies
3.3k
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
2
votes
4
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2.1k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by • 0
1
vote
1
reply
1.6k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.3 years ago Kajus Baidžajevas ▴ 10
1
vote
3
replies
3.0k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 8.5 years ago by ▴ 10 • written 8.5 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
1
vote
2
replies
1.5k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 16 months ago by ▴ 40 • written 4.0 years ago by ▴ 10
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
1
vote
1
reply
624
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by ▴ 10
1
vote
8
replies
2.2k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.1 years ago juls • 0
0
votes
0
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944
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
0
replies
757
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
2
replies
1.2k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 3.8 years ago by 65k • written 3.8 years ago by • 0
0
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0
replies
557
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
3.4 years ago paun_bio • 0
0
votes
0
replies
834
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.2 years ago Lluís Revilla Sancho ▴ 730
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 3.8k • written 2.3 years ago by ▴ 20
0
votes
0
replies
602
views
ReactomePA list of pathway plots
ReactomePA
23 months ago curiousmind007 ▴ 10
0
votes
0
replies
756
views
ReactomePA only showing 1 result
ReactomePA
4.9 years ago ayang • 0
0
votes
14
replies
3.3k
views
Error in ReactomePA
r reactomepa
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by ▴ 20
0
votes
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
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
1
reply
1.3k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
6.9 years ago bhgyu ▴ 30
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
2
replies
1.5k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
0
votes
2
replies
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
0
votes
5
replies
1.9k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
5.9 years ago martin.busch • 0
0
votes
0
replies
782
views
viewPathway not showing a gene of interest
ReactomePA
5.2 years ago santos22903 • 0
0
votes
1
reply
922
views
ReactomePA and genelist
ReactomePA
updated 5.0 years ago by • 0 • written 5.0 years ago by ▴ 10
0
votes
2
replies
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 4.4 years ago by 25k • written 4.4 years ago by • 0
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
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
0
votes
9
replies
1.6k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
3.8 years ago camillab. ▴ 10
0
votes
8
replies
2.5k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.0 years ago felix.thaler • 0
40 results • Page 1 of 1
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Answer: Citation for edgeR user guide by Gordon Smyth 50k
Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You are just making up data? What is the point of this exercise?
Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k
What do you mean by 'the information'? Do you have things in particular that you want?
Comment: minfi::read.metharray.exp by clacarion • 0
I think its work with `read.metharray.sheet` ```r > sheet <- read.metharray.sheet("/Users/clarachretienneau/Desktop/clock_epigenetic/PJ120…
Comment: minfi::read.metharray.exp by clacarion • 0
Thank you for your response Basti ! I add all the idat files in a unique folder called "idat" and add it in my path ```r > list.files("…
Votes
Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)
Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.
Answer: minfi::read.metharray.exp
Comment: Trying to use enrichGO
Answer: Cannabis OrgDb
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