Showing : reactomePA • reset
2
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3
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
10 months ago Yifeii.Ge • 0
1
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2
replies
2.3k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 2.8 years ago by ▴ 40 • written 5.4 years ago by ▴ 10
4
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4
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5.9k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.9 years ago by • 0 • written 9.0 years ago by ▴ 680
0
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0
replies
951
views
ReactomePA list of pathway plots
ReactomePA
3.2 years ago curiousmind007 ▴ 10
1
vote
1
reply
974
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by ▴ 20
0
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1
reply
2.0k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 3.6 years ago by 4.2k • written 3.6 years ago by ▴ 20
0
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0
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1.2k
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
4.5 years ago Lluís Revilla Sancho ▴ 760
3
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4
replies
3.4k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
4.5 years ago florianjt • 0
0
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0
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845
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.8 years ago paun_bio • 0
0
votes
2
replies
1.8k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 5.2 years ago by 68k • written 5.2 years ago by • 0
0
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9
replies
2.3k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
5.2 years ago camillab. ▴ 10
0
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0
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1.2k
views
reactomePA error input file
r reactomePA enrichment
updated 5.2 years ago by ★ 4.0k • written 5.2 years ago by ▴ 10
0
votes
0
replies
1.3k
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
5.3 years ago jan.soderman • 0
0
votes
8
replies
3.3k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
5.4 years ago felix.thaler • 0
0
votes
1
reply
5.2k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 5.4 years ago by ★ 1.2k • written 5.4 years ago by ▴ 10
0
votes
4
replies
3.1k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
votes
2
replies
2.8k
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 5.8 years ago by 25k • written 5.8 years ago by • 0
0
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0
replies
1000
views
ReactomePA only showing 1 result
ReactomePA
6.3 years ago ayang • 0
0
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1
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1.5k
views
ReactomePA and genelist
ReactomePA
updated 6.3 years ago by • 0 • written 6.3 years ago by ▴ 10
0
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0
replies
1.0k
views
viewPathway not showing a gene of interest
ReactomePA
6.6 years ago santos22903 • 0
2
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5
replies
4.6k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by ▴ 30
1
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2
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2.3k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
7.2 years ago martin.busch • 0
0
votes
5
replies
2.6k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
7.2 years ago martin.busch • 0
2
votes
4
replies
3.0k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 7.3 years ago by ★ 1.2k • written 7.3 years ago by • 0
0
votes
2
replies
2.8k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 7.4 years ago by ★ 1.2k • written 7.4 years ago by • 0
3
votes
5
replies
2.7k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
7.5 years ago thomasjenner333 • 0
0
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2
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2.1k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 7.6 years ago by ★ 1.2k • written 7.6 years ago by • 0
0
votes
3
replies
2.6k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
7.6 years ago andrew.gehrke • 0
3
votes
2
replies
7.1k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by ▴ 10
3
votes
4
replies
2.6k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 7.9 years ago by ▴ 150 • written 7.9 years ago by ▴ 10
3
votes
1
reply
1.5k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 8.2 years ago by ▴ 760 • written 8.2 years ago by • 0
0
votes
1
reply
1.7k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
8.2 years ago bhgyu ▴ 30
1
vote
8
replies
2.9k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
8.4 years ago juls • 0
1
vote
1
reply
1.9k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
8.6 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
2.4k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 8.6 years ago by ▴ 100 • written 8.6 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 8.9 years ago by 68k • written 8.9 years ago by • 0
1
vote
1
reply
1.8k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 8.9 years ago by ★ 1.2k • written 8.9 years ago by ▴ 10
0
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1
reply
2.3k
views
ReactomePA - Change colors in barplot
reactomepa
updated 9.0 years ago by ★ 1.2k • written 9.0 years ago by ▴ 860
0
votes
14
replies
4.3k
views
Error in ReactomePA
r reactomepa
updated 9.2 years ago by ★ 1.2k • written 9.2 years ago by ▴ 20
1
vote
3
replies
4.1k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 9.9 years ago by ▴ 10 • written 9.9 years ago by ▴ 10
2
votes
4
replies
2.7k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 10.4 years ago by ★ 1.2k • written 10.4 years ago by ▴ 140
41 results • Page 1 of 1
Recent ...
Replies
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I have checked DEGs between Solvent Control (SC) of FP and LP and there are noticebale differences in terms of DEGs. ``` # Checking SC in …
Answer: A0A287BB68 not recognized as UNPROT key in org.Ss.eg.db using AnnotationDbi::sel by James W. MacDonald 68k
Apparently it's been over-ridden by a different UniProtKB ID ``` > select(org.Ss.eg.db, "MYH11", "UNIPROT", "SYMBOL") 'select()' retu…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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