Showing : reactomepa • reset
5
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4
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Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 7.3 years ago by ▴ 100 • written 7.3 years ago by ▴ 40
4
votes
4
replies
4.2k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 18 months ago by • 0 • written 7.7 years ago by ▴ 660
3
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4
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2.3k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.2 years ago florianjt • 0
3
votes
4
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1.9k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 6.5 years ago by ▴ 150 • written 6.5 years ago by ▴ 10
3
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1
reply
1.2k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 6.8 years ago by ▴ 730 • written 6.8 years ago by • 0
3
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2
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4.8k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 6.5 years ago by ★ 1.2k • written 6.5 years ago by ▴ 10
3
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5
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2.0k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.1 years ago thomasjenner333 • 0
2
votes
4
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2.1k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 9.1 years ago by ★ 1.2k • written 9.1 years ago by ▴ 140
2
votes
5
replies
3.3k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 5.4 years ago by ★ 1.2k • written 5.4 years ago by ▴ 30
2
votes
4
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2.2k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 5.9 years ago by ★ 1.2k • written 5.9 years ago by • 0
1
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1
reply
1.6k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.3 years ago Kajus Baidžajevas ▴ 10
1
vote
3
replies
3.0k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 8.6 years ago by ▴ 10 • written 8.6 years ago by ▴ 10
1
vote
1
reply
1.5k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 7.6 years ago by ★ 1.2k • written 7.6 years ago by ▴ 10
1
vote
2
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1.5k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 17 months ago by ▴ 40 • written 4.0 years ago by ▴ 10
1
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2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.9 years ago martin.busch • 0
1
vote
1
reply
631
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by ▴ 10
1
vote
8
replies
2.2k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.1 years ago juls • 0
0
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0
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952
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
4.0 years ago jan.soderman • 0
0
votes
0
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763
views
reactomePA error input file
r reactomePA enrichment
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
0
votes
2
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1.2k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 3.8 years ago by 65k • written 3.9 years ago by • 0
0
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0
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561
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
3.4 years ago paun_bio • 0
0
votes
0
replies
841
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.2 years ago Lluís Revilla Sancho ▴ 730
0
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1
reply
1.3k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 2.3 years ago by 3.8k • written 2.3 years ago by ▴ 20
0
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0
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606
views
ReactomePA list of pathway plots
ReactomePA
23 months ago curiousmind007 ▴ 10
0
votes
0
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764
views
ReactomePA only showing 1 result
ReactomePA
4.9 years ago ayang • 0
0
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14
replies
3.3k
views
Error in ReactomePA
r reactomepa
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by ▴ 20
0
votes
1
reply
1.8k
views
ReactomePA - Change colors in barplot
reactomepa
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by ▴ 860
0
votes
1
reply
1.3k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 7.6 years ago by 65k • written 7.6 years ago by • 0
0
votes
1
reply
1.3k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
6.9 years ago bhgyu ▴ 30
0
votes
3
replies
1.9k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
0
votes
2
replies
1.6k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by • 0
0
votes
2
replies
2.0k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
0
votes
5
replies
1.9k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
5.9 years ago martin.busch • 0
0
votes
0
replies
791
views
viewPathway not showing a gene of interest
ReactomePA
5.2 years ago santos22903 • 0
0
votes
1
reply
937
views
ReactomePA and genelist
ReactomePA
updated 5.0 years ago by • 0 • written 5.0 years ago by ▴ 10
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 4.4 years ago by 25k • written 4.4 years ago by • 0
0
votes
4
replies
1.3k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 4.2 years ago by 65k • written 4.2 years ago by • 0
0
votes
1
reply
4.0k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 4.1 years ago by ★ 1.2k • written 4.1 years ago by ▴ 10
0
votes
9
replies
1.6k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
3.9 years ago camillab. ▴ 10
0
votes
8
replies
2.5k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.0 years ago felix.thaler • 0
40 results • Page 1 of 1
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Answer: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k
This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…
Answer: Get genomic coordinates of CpGs sites (chromosomes, genomic position) by James W. MacDonald 65k
You don't say what array that is, so I will guess. ``` > library(IlluminaHumanMethylationEPICanno.ilm10b4.hg19) > Locations DataFrame…
Answer: SGSeq: moving toward diffex from SGSeq analysis by Leonard Goldstein ▴ 200
`vid` and `eid` are unique identifiers for splice variants and splicing events respectively. They are analogous to exon bin and gene identi…
Comment: Help with error using camera() in limma by Chris • 0
Thanks James! I fixed the error. I try gene symbol instead of entrez and it worked.
Comment: limma for gene expression analysis with big and unbalanced sample size by XW • 0
Could you explain more about the comment "there are no problems with using limma for unbalanced data sets" ? thanks.
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SPIA plotP giving error
Answer: Fold change calculation in Diffbind vs. DESEQ2?
C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB
C: Extremely big genes in annotation TxDb packages
Make custom Txdb class objects from Txdb
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