Showing : reactomepa • reset
2
votes
3
replies
672
views
Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
7 weeks ago Yifeii.Ge • 0
1
vote
2
replies
1.9k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 2.0 years ago by ▴ 40 • written 4.6 years ago by ▴ 10
4
votes
4
replies
5.1k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.2 years ago by • 0 • written 8.3 years ago by ▴ 660
0
votes
0
replies
786
views
ReactomePA list of pathway plots
ReactomePA
2.5 years ago curiousmind007 ▴ 10
1
vote
1
reply
815
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.7 years ago by ▴ 780 • written 2.7 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 2.9 years ago by 4.1k • written 2.9 years ago by ▴ 20
0
votes
0
replies
987
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.8 years ago Lluís Revilla Sancho ▴ 760
3
votes
4
replies
2.9k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.8 years ago florianjt • 0
0
votes
0
replies
710
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.1 years ago paun_bio • 0
0
votes
2
replies
1.5k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
0
votes
9
replies
2.0k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.5 years ago camillab. ▴ 10
0
votes
0
replies
937
views
reactomePA error input file
r reactomePA enrichment
updated 4.5 years ago by ★ 4.0k • written 4.5 years ago by ▴ 10
0
votes
0
replies
1.2k
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
4.7 years ago felix.thaler • 0
0
votes
1
reply
4.6k
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
2.1k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 4.8 years ago by 67k • written 4.8 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
votes
0
replies
888
views
ReactomePA only showing 1 result
ReactomePA
5.6 years ago ayang • 0
0
votes
1
reply
1.2k
views
ReactomePA and genelist
ReactomePA
updated 5.6 years ago by • 0 • written 5.6 years ago by ▴ 10
0
votes
0
replies
909
views
viewPathway not showing a gene of interest
ReactomePA
5.9 years ago santos22903 • 0
2
votes
5
replies
4.0k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 6.0 years ago by ★ 1.2k • written 6.0 years ago by ▴ 30
1
vote
2
replies
2.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.5 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 6.6 years ago by ★ 1.2k • written 6.6 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
votes
5
replies
2.3k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.8 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 6.9 years ago by ★ 1.2k • written 6.9 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
5.9k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.1 years ago by ★ 1.2k • written 7.1 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
1.4k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 7.5 years ago by ▴ 760 • written 7.5 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
2.1k
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 8.2 years ago by 67k • written 8.2 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 8.5 years ago by ★ 1.2k • written 8.5 years ago by ▴ 20
1
vote
3
replies
3.6k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 9.2 years ago by ▴ 10 • written 9.2 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
Recent ...
Replies
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Just fit a model `~condition + experiment` where `condition` has three levels A, B and C. Ideally, use limma and include duplicate correlat…
Comment: Error in get_anno_data(ontology) : ontology not supported yet... by GODseeker • 0
thank u so much ,god bless u,my dear friend.
Comment: Feature Counts - potential bug with outfile.jcounts by chris2.a.white • 0
Hi @gordonsmyth and @weishi, Firstly, thank you for offering your time to develop the junction quantification module further. This is gre…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Hi Tim, Thanks for your reply! Yes, my data is 450K, and it is TCGA methylation data downloaded by TCGAbiolinks. The problem is that I can …
Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k
Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…
Votes
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
Answer: Can we get beta values with DMRcate package
DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)
Awards • All
Popular Question to martin.grigorov ▴ 10
Scholar to James W. MacDonald 67k
Popular Question to Benjamin ▴ 20
Popular Question to María Calvo • 0
Popular Question to Gordon Smyth 52k
Locations • All
WEHI, Melbourne, Australia, just now
The city by the bay, just now
New York,NY,USA, 1 minute ago
France, 2 minutes ago
Australia, 4 minutes ago
Traffic: 974 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