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ReactomePA
•
reset
0
votes
0
replies
577
views
ReactomePA list of pathway plots
ReactomePA
22 months ago
curiousmind007
▴ 10
1
vote
1
reply
601
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler
ReactomePA
updated 23 months ago by
Basti
▴ 750 • written 23 months ago by
charlesgwellem
▴ 10
0
votes
1
reply
1.2k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA
package
annotation
updated 2.2 years ago by
shepherl
3.8k • written 2.2 years ago by
mathavanbioinfo
▴ 20
0
votes
0
replies
807
views
enrichPathway error when checking condition lengths used
DOSE
ReactomePA
3.1 years ago
Lluís Revilla Sancho
▴ 730
3
votes
4
replies
2.2k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db
ReactomePA
3.1 years ago
florianjt
• 0
0
votes
0
replies
545
views
Clusterprofiler - best practise for missing ids
ReactomePA
clusterProfiler
GeneSetEnrichment
3.4 years ago
paun_bio
• 0
0
votes
2
replies
1.2k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview
ReactomePA
updated 3.8 years ago by
James W. MacDonald
65k • written 3.8 years ago by
emisecherre
• 0
0
votes
9
replies
1.5k
views
ReactomePA error graph
r
rnaseq
bulk
GO
ReactomePA
3.8 years ago
camillab.
▴ 10
0
votes
0
replies
746
views
reactomePA error input file
r
reactomePA
enrichment
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
camillab.
▴ 10
0
votes
0
replies
920
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot
ReactomePA
clusterProfiler
similarity coefficients
emapplot
3.9 years ago
jan.soderman
• 0
1
vote
2
replies
1.5k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway
ReactomePA
updated 16 months ago by
landenshanie
▴ 40 • written 3.9 years ago by
DataFanatic
▴ 10
0
votes
8
replies
2.4k
views
Adding Enrichresults for creating plot
ReactomePA
clusterProfiler
3.9 years ago
felix.thaler
• 0
0
votes
1
reply
3.9k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler
ReactomePA
updated 4.0 years ago by
Guangchuang Yu
★ 1.2k • written 4.0 years ago by
liampvmartin1992
▴ 10
0
votes
4
replies
1.2k
views
How to list all "..." parameters inside R function
ReactomePA
clusterProfiler
updated 4.1 years ago by
James W. MacDonald
65k • written 4.1 years ago by
lucap
• 0
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 4.3 years ago by
Martin Morgan
25k • written 4.3 years ago by
goodwinjinesh
• 0
0
votes
0
replies
743
views
ReactomePA only showing 1 result
ReactomePA
4.8 years ago
ayang
• 0
0
votes
1
reply
894
views
ReactomePA and genelist
ReactomePA
updated 4.9 years ago by
saicharanp18
• 0 • written 4.9 years ago by
Merlin
▴ 10
0
votes
0
replies
768
views
viewPathway not showing a gene of interest
ReactomePA
5.1 years ago
santos22903
• 0
2
votes
5
replies
3.2k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 5.3 years ago by
Guangchuang Yu
★ 1.2k • written 5.3 years ago by
dorothy.jrobbert
▴ 30
1
vote
2
replies
1.7k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
5.8 years ago
martin.busch
• 0
0
votes
5
replies
1.8k
views
ReactomePA / Reactome: Crash when plotting
reactomepa
reactomepa reactome bioconductor viewpathway
reactome.db
reactome
5.8 years ago
martin.busch
• 0
2
votes
4
replies
2.1k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways
reactomepa
functional annotation
updated 5.9 years ago by
Guangchuang Yu
★ 1.2k • written 5.9 years ago by
martin.busch
• 0
0
votes
2
replies
1.9k
views
p-values in Reactome and ReactomePA
reactomepa
reactome
updated 6.0 years ago by
Guangchuang Yu
★ 1.2k • written 6.0 years ago by
heir_of_isildur88
• 0
3
votes
5
replies
1.9k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa
clusterprofiler
6.0 years ago
thomasjenner333
• 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
Guangchuang Yu
★ 1.2k • written 6.2 years ago by
jan.soderman
• 0
0
votes
3
replies
1.9k
views
custom background list for ReactomePA
reactomepa
chipseeker
Guangchuang Yu
6.2 years ago
andrew.gehrke
• 0
3
votes
2
replies
4.6k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa
pathway analysis
enrichment analysis
clusterprofiler
updated 6.4 years ago by
Guangchuang Yu
★ 1.2k • written 6.4 years ago by
Miguel.Cosenza
▴ 10
3
votes
4
replies
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 6.4 years ago by
willem.ligtenberg
▴ 150 • written 6.4 years ago by
Miguel.Cosenza
▴ 10
3
votes
1
reply
1.1k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 6.8 years ago by
Lluís Revilla Sancho
▴ 730 • written 6.8 years ago by
juls
• 0
0
votes
1
reply
1.3k
views
GSEA threshold question
GSEa
r
clusterprofiler
reactomepa
6.8 years ago
bhgyu
▴ 30
1
vote
8
replies
2.2k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.0 years ago
juls
• 0
1
vote
1
reply
1.5k
views
ReactomePA viewPathway DE node and legend colour
DOSE
ReactomePA
7.2 years ago
Kajus Baidžajevas
▴ 10
5
votes
4
replies
1.7k
views
Reactome pathways in ReactomeDB/graphite
reactomepa
reactome
graphite
updated 7.2 years ago by
gabriele.sales
▴ 100 • written 7.2 years ago by
i.sudbery
▴ 30
0
votes
1
reply
1.3k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 7.5 years ago by
James W. MacDonald
65k • written 7.5 years ago by
elitemao
• 0
1
vote
1
reply
1.5k
views
how to link ReactomePA with DESeq2
ReactomePA
GO
updated 7.5 years ago by
Guangchuang Yu
★ 1.2k • written 7.5 years ago by
ta_awwad
▴ 10
4
votes
4
replies
4.1k
views
Clarifications on p-values in enrichResult objects
clusterProfiler
reactomepa
dose
updated 17 months ago by
12133067
• 0 • written 7.6 years ago by
enricoferrero
▴ 660
0
votes
1
reply
1.8k
views
ReactomePA - Change colors in barplot
reactomepa
updated 7.6 years ago by
Guangchuang Yu
★ 1.2k • written 7.6 years ago by
David
▴ 860
0
votes
14
replies
3.3k
views
Error in ReactomePA
r
reactomepa
updated 7.7 years ago by
Guangchuang Yu
★ 1.2k • written 7.7 years ago by
Ram
▴ 20
1
vote
3
replies
3.0k
views
Reactome pathway analysis using ReactomePA
reactomepa
R
bioconductor
ReactomePA
updated 8.5 years ago by
kmezhoud
▴ 10 • written 8.5 years ago by
Deepak Tanwar
▴ 10
2
votes
4
replies
2.1k
views
ReactomePA : error with gsePathway
ReactomePA
gsePathway
updated 9.0 years ago by
Guangchuang Yu
★ 1.2k • written 9.0 years ago by
samuel collombet
▴ 140
40 results • Page
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Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
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Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Comment: fgsea fork
by
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3.8k
Not quite sure what you mean by clone or fork the package on latest version of R. Bioconductor runs all builds on the latest version of R.…
Answer: Doing comparison of RNA-seq data using EdgeR
by
Gordon Smyth
50k
It's pretty easy to do a two-group comparison using edgeR, but you seem to be stuck at the initial stage of reading data into R. If you exp…
Answer: Differing results from plotMDS and PCAtools
by
Gordon Smyth
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The reason why the two plots are different is that the first plot is a PCA plot while the second is a biplot. Quite different plots. The P…
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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