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reactomePA
•
reset
0
votes
0
replies
68
views
ReactomePA list of pathway plots
ReactomePA
10 weeks ago
curiousmind007
• 0
1
vote
1
reply
135
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler
ReactomePA
updated 3 months ago by
Basti
▴ 390 • written 3 months ago by
charlesgwellem
▴ 10
0
votes
1
reply
359
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA
package
annotation
updated 7 months ago by
shepherl
3.2k • written 7 months ago by
mathavanbioinfo
▴ 20
0
votes
0
replies
313
views
enrichPathway error when checking condition lengths used
DOSE
ReactomePA
17 months ago
Lluís Revilla Sancho
▴ 690
3
votes
4
replies
633
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db
ReactomePA
18 months ago
florianjt
• 0
0
votes
0
replies
272
views
Clusterprofiler - best practise for missing ids
ReactomePA
clusterProfiler
GeneSetEnrichment
21 months ago
paun_bio
• 0
0
votes
2
replies
455
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview
ReactomePA
updated 2.1 years ago by
James W. MacDonald
60k • written 2.1 years ago by
emisecherre
• 0
0
votes
9
replies
672
views
ReactomePA error graph
r
rnaseq
bulk
GO
ReactomePA
2.1 years ago
camillab.
▴ 10
0
votes
0
replies
380
views
reactomePA error input file
r
reactomePA
enrichment
updated 2.2 years ago by
Kevin Blighe
3.6k • written 2.2 years ago by
camillab.
▴ 10
0
votes
0
replies
387
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot
ReactomePA
clusterProfiler
similarity coefficients
emapplot
2.3 years ago
jan.soderman
• 0
1
vote
1
reply
526
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway
ReactomePA
updated 2.3 years ago by
Kevin Blighe
3.6k • written 2.3 years ago by
DataFanatic
• 0
0
votes
8
replies
1.1k
views
Adding Enrichresults for creating plot
ReactomePA
clusterProfiler
2.3 years ago
felix.thaler
• 0
0
votes
1
reply
1.9k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler
ReactomePA
updated 2.4 years ago by
Guangchuang Yu
★ 1.2k • written 2.4 years ago by
liampvmartin1992
▴ 10
0
votes
4
replies
470
views
How to list all "..." parameters inside R function
ReactomePA
clusterProfiler
updated 2.5 years ago by
James W. MacDonald
60k • written 2.5 years ago by
lucap
• 0
0
votes
2
replies
1.1k
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 2.7 years ago by
Martin Morgan
25k • written 2.7 years ago by
goodwinjinesh
• 0
0
votes
0
replies
454
views
ReactomePA only showing 1 result
ReactomePA
3.2 years ago
ayang
• 0
0
votes
1
reply
437
views
ReactomePA and genelist
ReactomePA
updated 3.3 years ago by
saicharanp18
• 0 • written 3.3 years ago by
Merlin
▴ 10
0
votes
0
replies
433
views
viewPathway not showing a gene of interest
ReactomePA
3.5 years ago
santos22903
• 0
2
votes
5
replies
1.9k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 3.7 years ago by
Guangchuang Yu
★ 1.2k • written 3.7 years ago by
dorothy.jrobbert
▴ 20
1
vote
2
replies
1.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
4.2 years ago
martin.busch
• 0
0
votes
5
replies
1.1k
views
ReactomePA / Reactome: Crash when plotting
reactomepa
reactomepa reactome bioconductor viewpathway
reactome.db
reactome
4.2 years ago
martin.busch
• 0
2
votes
4
replies
1.1k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways
reactomepa
functional annotation
updated 4.2 years ago by
Guangchuang Yu
★ 1.2k • written 4.2 years ago by
martin.busch
• 0
0
votes
2
replies
1.1k
views
p-values in Reactome and ReactomePA
reactomepa
reactome
updated 4.4 years ago by
Guangchuang Yu
★ 1.2k • written 4.4 years ago by
heir_of_isildur88
• 0
3
votes
5
replies
1.1k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa
clusterprofiler
4.4 years ago
thomasjenner333
• 0
0
votes
2
replies
938
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE
ReactomePA
enrichMap
enrichPathway
updated 4.5 years ago by
Guangchuang Yu
★ 1.2k • written 4.5 years ago by
jan.soderman
• 0
0
votes
3
replies
1.1k
views
custom background list for ReactomePA
reactomepa
chipseeker
Guangchuang Yu
4.6 years ago
andrew.gehrke
• 0
3
votes
2
replies
2.6k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa
pathway analysis
enrichment analysis
clusterprofiler
updated 4.8 years ago by
Guangchuang Yu
★ 1.2k • written 4.8 years ago by
Miguel.Cosenza
▴ 10
3
votes
4
replies
1.1k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa
reactome.db
reactome
proteomics
uniprot accessions
updated 4.8 years ago by
willem.ligtenberg
▴ 150 • written 4.8 years ago by
Miguel.Cosenza
▴ 10
3
votes
1
reply
732
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 5.1 years ago by
Lluís Revilla Sancho
▴ 690 • written 5.1 years ago by
juls
• 0
0
votes
1
reply
845
views
GSEA threshold question
GSEa
r
clusterprofiler
reactomepa
5.2 years ago
bhgyu
▴ 30
1
vote
8
replies
1.3k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
5.4 years ago
juls
• 0
1
vote
1
reply
1.1k
views
ReactomePA viewPathway DE node and legend colour
DOSE
ReactomePA
5.6 years ago
Kajus Baidžajevas
▴ 10
5
votes
4
replies
1.1k
views
Reactome pathways in ReactomeDB/graphite
reactomepa
reactome
graphite
updated 5.6 years ago by
gabriele.sales
▴ 100 • written 5.6 years ago by
i.sudbery
▴ 30
0
votes
1
reply
964
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 5.9 years ago by
James W. MacDonald
60k • written 5.9 years ago by
elitemao
• 0
1
vote
1
reply
1.1k
views
how to link ReactomePA with DESeq2
ReactomePA
GO
updated 5.9 years ago by
Guangchuang Yu
★ 1.2k • written 5.9 years ago by
ta_awwad
▴ 10
4
votes
3
replies
1.6k
views
Clarifications on p-values in enrichResult objects
clusterProfiler
reactomepa
dose
updated 6.0 years ago by
Guangchuang Yu
★ 1.2k • written 6.0 years ago by
enricoferrero
▴ 620
0
votes
1
reply
1.1k
views
ReactomePA - Change colors in barplot
reactomepa
updated 6.0 years ago by
Guangchuang Yu
★ 1.2k • written 6.0 years ago by
David
▴ 860
0
votes
14
replies
2.2k
views
Error in ReactomePA
r
reactomepa
updated 6.1 years ago by
Guangchuang Yu
★ 1.2k • written 6.1 years ago by
Ram
▴ 20
1
vote
3
replies
1.9k
views
Reactome pathway analysis using ReactomePA
reactomepa
R
bioconductor
ReactomePA
updated 6.8 years ago by
kmezhoud
▴ 10 • written 6.8 years ago by
Deepak Tanwar
▴ 10
2
votes
4
replies
1.6k
views
ReactomePA : error with gsePathway
ReactomePA
gsePathway
updated 7.4 years ago by
Guangchuang Yu
★ 1.2k • written 7.4 years ago by
samuel collombet
▴ 140
40 results • Page
1 of 1
Recent ...
Replies
Comment: Design and contrast matrices for analyzing the effect of two factors of interest
by
Gordon Smyth
46k
I understand that your mock dataset has expression data for just one protein instead of 8000, but is the phenoData complete? Does your real…
Comment: error running UniProt.ws
by
James W. MacDonald
60k
Or maybe it is a quick fix! Nicely done Marcel!
Answer: Error with TCGA package - TCGAbiolinks
by
Tiago C. Silva
▴ 220
It is working with the github version. Could you update please? BiocManager::install("BioinformaticsFMRP/TCGAbiolinksGUI.data") …
Comment: Error with TCGA package - TCGAbiolinks
by
Marcel Ramos
570
You can try the Genomic Data Commons Data Portal at [https://portal.gdc.cancer.gov/][1] or the `GenomicDataCommons` R/Bioconductor packag…
Answer: error running UniProt.ws
by
Marcel Ramos
570
I've updated the package to handle these requests on both Bioc devel and release 3.15. Let me know if you have any issues. Best, M…
Votes
A: Importance of Order in Design Formula
remove microarray batch effects using Limma
On empirical Bayes of edgeR
Answer: CQN to DESeq2
Comment: package 'BiocInstaller' is not available (for R version 3.4.4)
Awards
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Marcel Ramos
570
Scholar
to
Gordon Smyth
46k
Popular Question
to
sunnykevin97
• 0
Popular Question
to
Alejandro Reyes
★ 1.8k
Popular Question
to
Leonardo Collado Torres
▴ 1000
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