Showing : ReactomePA • reset
2
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Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
7 weeks ago Yifeii.Ge • 0
1
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2
replies
1.9k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 2.1 years ago by ▴ 40 • written 4.7 years ago by ▴ 10
4
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4
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5.1k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.2 years ago by • 0 • written 8.3 years ago by ▴ 660
0
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0
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792
views
ReactomePA list of pathway plots
ReactomePA
2.6 years ago curiousmind007 ▴ 10
1
vote
1
reply
819
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by ▴ 10
0
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1
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1.6k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 2.9 years ago by 4.1k • written 2.9 years ago by ▴ 20
0
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0
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989
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.8 years ago Lluís Revilla Sancho ▴ 760
3
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4
replies
2.9k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.8 years ago florianjt • 0
0
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0
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712
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.1 years ago paun_bio • 0
0
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2
replies
1.5k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 4.5 years ago by 67k • written 4.5 years ago by • 0
0
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9
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2.0k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.5 years ago camillab. ▴ 10
0
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0
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938
views
reactomePA error input file
r reactomePA enrichment
updated 4.6 years ago by ★ 4.0k • written 4.6 years ago by ▴ 10
0
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0
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1.2k
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
4.6 years ago jan.soderman • 0
0
votes
8
replies
2.9k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.7 years ago felix.thaler • 0
0
votes
1
reply
4.6k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 4.7 years ago by ★ 1.2k • written 4.7 years ago by ▴ 10
0
votes
4
replies
2.1k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 4.8 years ago by 67k • written 4.8 years ago by • 0
0
votes
2
replies
2.4k
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 5.1 years ago by 25k • written 5.1 years ago by • 0
0
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0
replies
889
views
ReactomePA only showing 1 result
ReactomePA
5.6 years ago ayang • 0
0
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1
reply
1.2k
views
ReactomePA and genelist
ReactomePA
updated 5.6 years ago by • 0 • written 5.7 years ago by ▴ 10
0
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0
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912
views
viewPathway not showing a gene of interest
ReactomePA
5.9 years ago santos22903 • 0
2
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5
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4.0k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 6.0 years ago by ★ 1.2k • written 6.0 years ago by ▴ 30
1
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2
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2.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.5 years ago martin.busch • 0
0
votes
5
replies
2.2k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
6.5 years ago martin.busch • 0
2
votes
4
replies
2.6k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.6 years ago by ★ 1.2k • written 6.6 years ago by • 0
0
votes
2
replies
2.4k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by • 0
3
votes
5
replies
2.4k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.8 years ago thomasjenner333 • 0
0
votes
2
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1.8k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
0
votes
3
replies
2.3k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
7.0 years ago • updated 6.9 years ago andrew.gehrke • 0
3
votes
2
replies
6.0k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by ▴ 10
3
votes
4
replies
2.2k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ▴ 10
3
votes
1
reply
1.4k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 7.5 years ago by ▴ 760 • written 7.5 years ago by • 0
0
votes
1
reply
1.5k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
7.5 years ago bhgyu ▴ 30
1
vote
8
replies
2.6k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.7 years ago juls • 0
1
vote
1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
7.9 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
2.1k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 7.9 years ago by ▴ 100 • written 7.9 years ago by ▴ 40
0
votes
1
reply
1.4k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 8.2 years ago by 67k • written 8.2 years ago by • 0
1
vote
1
reply
1.7k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 8.2 years ago by ★ 1.2k • written 8.2 years ago by ▴ 10
0
votes
1
reply
2.1k
views
ReactomePA - Change colors in barplot
reactomepa
updated 8.3 years ago by ★ 1.2k • written 8.3 years ago by ▴ 860
0
votes
14
replies
3.8k
views
Error in ReactomePA
r reactomepa
updated 8.5 years ago by ★ 1.2k • written 8.5 years ago by ▴ 20
1
vote
3
replies
3.6k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 9.2 years ago by ▴ 10 • written 9.2 years ago by ▴ 10
2
votes
4
replies
2.4k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 9.8 years ago by ★ 1.2k • written 9.8 years ago by ▴ 140
41 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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