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reactomepa
•
reset
2
votes
3
replies
1.1k
views
Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE
ReactomePA
4 months ago
Yifeii.Ge
• 0
1
vote
2
replies
2.1k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway
ReactomePA
updated 2.3 years ago by
landenshanie
▴ 40 • written 4.9 years ago by
DataFanatic
▴ 10
4
votes
4
replies
5.5k
views
Clarifications on p-values in enrichResult objects
clusterProfiler
reactomepa
dose
updated 2.4 years ago by
12133067
• 0 • written 8.6 years ago by
enricoferrero
▴ 680
0
votes
0
replies
862
views
ReactomePA list of pathway plots
ReactomePA
2.8 years ago
curiousmind007
▴ 10
1
vote
1
reply
876
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler
ReactomePA
updated 2.9 years ago by
Basti
▴ 780 • written 2.9 years ago by
charlesgwellem
▴ 10
0
votes
1
reply
1.8k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA
package
annotation
updated 3.2 years ago by
shepherl
4.1k • written 3.2 years ago by
mathavanbioinfo
▴ 20
0
votes
0
replies
1.0k
views
enrichPathway error when checking condition lengths used
DOSE
ReactomePA
4.1 years ago
Lluís Revilla Sancho
▴ 760
3
votes
4
replies
3.1k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db
ReactomePA
4.1 years ago
florianjt
• 0
0
votes
0
replies
758
views
Clusterprofiler - best practise for missing ids
ReactomePA
clusterProfiler
GeneSetEnrichment
4.3 years ago
paun_bio
• 0
0
votes
2
replies
1.6k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview
ReactomePA
updated 4.7 years ago by
James W. MacDonald
68k • written 4.7 years ago by
emisecherre
• 0
0
votes
9
replies
2.1k
views
ReactomePA error graph
r
rnaseq
bulk
GO
ReactomePA
4.8 years ago
camillab.
▴ 10
0
votes
0
replies
999
views
reactomePA error input file
r
reactomePA
enrichment
updated 4.8 years ago by
Kevin Blighe
★ 4.0k • written 4.8 years ago by
camillab.
▴ 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
4.9 years ago
jan.soderman
• 0
0
votes
8
replies
3.1k
views
Adding Enrichresults for creating plot
ReactomePA
clusterProfiler
4.9 years ago
felix.thaler
• 0
0
votes
1
reply
4.9k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler
ReactomePA
updated 5.0 years ago by
Guangchuang Yu
★ 1.2k • written 5.0 years ago by
liampvmartin1992
▴ 10
0
votes
4
replies
2.6k
views
How to list all "..." parameters inside R function
ReactomePA
clusterProfiler
updated 5.1 years ago by
James W. MacDonald
68k • written 5.1 years ago by
lucap
• 0
0
votes
2
replies
2.6k
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 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
goodwinjinesh
• 0
0
votes
0
replies
932
views
ReactomePA only showing 1 result
ReactomePA
5.8 years ago
ayang
• 0
0
votes
1
reply
1.3k
views
ReactomePA and genelist
ReactomePA
updated 5.9 years ago by
saicharanp18
• 0 • written 5.9 years ago by
Merlin
▴ 10
0
votes
0
replies
957
views
viewPathway not showing a gene of interest
ReactomePA
6.1 years ago
santos22903
• 0
2
votes
5
replies
4.3k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 6.3 years ago by
Guangchuang Yu
★ 1.2k • written 6.3 years ago by
dorothy.jrobbert
▴ 30
1
vote
2
replies
2.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa
reactome
gsea
fgsea
6.8 years ago
martin.busch
• 0
0
votes
5
replies
2.4k
views
ReactomePA / Reactome: Crash when plotting
reactomepa
reactomepa reactome bioconductor viewpathway
reactome.db
reactome
6.8 years ago
martin.busch
• 0
2
votes
4
replies
2.8k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways
reactomepa
functional annotation
updated 6.8 years ago by
Guangchuang Yu
★ 1.2k • written 6.8 years ago by
martin.busch
• 0
0
votes
2
replies
2.5k
views
p-values in Reactome and ReactomePA
reactomepa
reactome
updated 7.0 years ago by
Guangchuang Yu
★ 1.2k • written 7.0 years ago by
heir_of_isildur88
• 0
3
votes
5
replies
2.5k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa
clusterprofiler
7.0 years ago
thomasjenner333
• 0
0
votes
2
replies
1.9k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE
ReactomePA
enrichMap
enrichPathway
updated 7.2 years ago by
Guangchuang Yu
★ 1.2k • written 7.2 years ago by
jan.soderman
• 0
0
votes
3
replies
2.4k
views
custom background list for ReactomePA
reactomepa
chipseeker
Guangchuang Yu
7.2 years ago
andrew.gehrke
• 0
3
votes
2
replies
6.4k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa
pathway analysis
enrichment analysis
clusterprofiler
updated 7.4 years ago by
Guangchuang Yu
★ 1.2k • written 7.4 years ago by
Miguel.Cosenza
▴ 10
3
votes
4
replies
2.4k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa
reactome.db
reactome
proteomics
uniprot accessions
updated 7.4 years ago by
willem.ligtenberg
▴ 150 • written 7.4 years ago by
Miguel.Cosenza
▴ 10
3
votes
1
reply
1.4k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 7.7 years ago by
Lluís Revilla Sancho
▴ 760 • written 7.7 years ago by
juls
• 0
0
votes
1
reply
1.6k
views
GSEA threshold question
GSEa
r
clusterprofiler
reactomepa
7.8 years ago
bhgyu
▴ 30
1
vote
8
replies
2.7k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
8.0 years ago
juls
• 0
1
vote
1
reply
1.9k
views
ReactomePA viewPathway DE node and legend colour
DOSE
ReactomePA
8.2 years ago
Kajus Baidžajevas
▴ 10
5
votes
4
replies
2.2k
views
Reactome pathways in ReactomeDB/graphite
reactomepa
reactome
graphite
updated 8.2 years ago by
gabriele.sales
▴ 100 • written 8.2 years ago by
i.sudbery
▴ 40
0
votes
1
reply
1.5k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 8.5 years ago by
James W. MacDonald
68k • written 8.5 years ago by
elitemao
• 0
1
vote
1
reply
1.7k
views
how to link ReactomePA with DESeq2
ReactomePA
GO
updated 8.5 years ago by
Guangchuang Yu
★ 1.2k • written 8.5 years ago by
ta_awwad
▴ 10
0
votes
1
reply
2.2k
views
ReactomePA - Change colors in barplot
reactomepa
updated 8.6 years ago by
Guangchuang Yu
★ 1.2k • written 8.6 years ago by
David
▴ 860
0
votes
14
replies
4.0k
views
Error in ReactomePA
r
reactomepa
updated 8.7 years ago by
Guangchuang Yu
★ 1.2k • written 8.7 years ago by
Ram
▴ 20
1
vote
3
replies
3.8k
views
Reactome pathway analysis using ReactomePA
reactomepa
R
bioconductor
ReactomePA
updated 9.4 years ago by
kmezhoud
▴ 10 • written 9.5 years ago by
Deepak Tanwar
▴ 10
2
votes
4
replies
2.5k
views
ReactomePA : error with gsePathway
ReactomePA
gsePathway
updated 10.0 years ago by
Guangchuang Yu
★ 1.2k • written 10.0 years ago by
samuel collombet
▴ 140
41 results • Page
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Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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