Showing : ReactomePA • reset
2
votes
3
replies
494
views
Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
8 days ago • updated 7 days ago Yifeii.Ge • 0
1
vote
2
replies
1.8k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 23 months ago by ▴ 40 • written 4.5 years ago by ▴ 10
4
votes
4
replies
4.9k
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
votes
0
replies
762
views
ReactomePA list of pathway plots
ReactomePA
2.4 years ago curiousmind007 ▴ 10
1
vote
1
reply
788
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.5 years ago by ▴ 780 • written 2.5 years ago by ▴ 10
0
votes
1
reply
1.6k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 2.8 years ago by 4.1k • written 2.8 years ago by ▴ 20
0
votes
0
replies
969
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.7 years ago Lluís Revilla Sancho ▴ 760
3
votes
4
replies
2.8k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.7 years ago florianjt • 0
0
votes
0
replies
690
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
votes
9
replies
1.9k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.4 years ago camillab. ▴ 10
0
votes
0
replies
917
views
reactomePA error input file
r reactomePA enrichment
updated 4.4 years ago by ★ 4.0k • written 4.4 years ago by ▴ 10
0
votes
0
replies
1.1k
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
4.5 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 4.6 years ago by ★ 1.2k • written 4.6 years ago by ▴ 10
0
votes
4
replies
1.9k
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
2.3k
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 4.9 years ago by 25k • written 4.9 years ago by • 0
0
votes
0
replies
873
views
ReactomePA only showing 1 result
ReactomePA
5.4 years ago ayang • 0
0
votes
1
reply
1.1k
views
ReactomePA and genelist
ReactomePA
updated 5.5 years ago by • 0 • written 5.5 years ago by ▴ 10
0
votes
0
replies
884
views
viewPathway not showing a gene of interest
ReactomePA
5.8 years ago santos22903 • 0
2
votes
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 5.9 years ago by ▴ 30
1
vote
2
replies
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
6.4 years ago martin.busch • 0
2
votes
4
replies
2.5k
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 6.6 years ago by ★ 1.2k • written 6.6 years ago by • 0
3
votes
5
replies
2.3k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.7 years ago thomasjenner333 • 0
0
votes
2
replies
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
2.2k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.8 years ago andrew.gehrke • 0
3
votes
2
replies
5.7k
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
2.1k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 7.0 years ago by ▴ 150 • written 7.0 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
7.4 years ago bhgyu ▴ 30
1
vote
8
replies
2.5k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.6 years ago juls • 0
1
vote
1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.8 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
2.0k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 7.8 years ago by ▴ 100 • written 7.8 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 8.1 years ago by ★ 1.2k • written 8.1 years ago by ▴ 10
0
votes
1
reply
2.1k
views
ReactomePA - Change colors in barplot
reactomepa
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 860
0
votes
14
replies
3.7k
views
Error in ReactomePA
r reactomepa
updated 8.3 years ago by ★ 1.2k • written 8.3 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 9.6 years ago by ★ 1.2k • written 9.6 years ago by ▴ 140
41 results • Page 1 of 1
Recent ...
Replies
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Fahd • 0
Thanks for looking into this. This issue results in the incorrect usage of multiple ORA software including EnrichR.
Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k
Yes, I understand the implications of replacing the `OrgDb` packages in release. Maybe an upload to the annotationHub or GitHub could be an…
Votes
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
Awards • All
Popular Question to Mikhail Dozmorov ▴ 30
Popular Question to Gordon Smyth 51k
Popular Question to Rohmatul • 0
Popular Question to Denise • 0
Popular Question to Assa Yeroslaviz ★ 1.5k
Locations • All
France, 2 minutes ago
United States, 38 minutes ago
The city by the bay, 47 minutes ago
University of Chicago, 47 minutes ago
WEHI, Melbourne, Australia, 2 hours ago
Traffic: 470 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6