Showing : reactomePA • reset
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enrichPathway error when checking condition lengths used
DOSE ReactomePA
8 months ago Lluís Revilla Sancho ▴ 650
3
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4
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306
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Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
8 months ago florianjt • 0
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0
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170
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Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
11 months ago paun_bio • 0
0
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2
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237
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Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 16 months ago by 58k • written 16 months ago by • 0
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9
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453
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ReactomePA error graph
r rnaseq bulk GO ReactomePA
16 months ago camillab. ▴ 10
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212
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reactomePA error input file
r reactomePA enrichment
updated 16 months ago by 3.4k • written 16 months ago by ▴ 10
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254
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similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
17 months ago jan.soderman • 0
1
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1
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329
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ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 18 months ago by 3.4k • written 18 months ago by • 0
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8
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706
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Adding Enrichresults for creating plot
ReactomePA clusterProfiler
18 months ago felix.thaler • 0
0
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1
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925
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How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 19 months ago by ★ 1.2k • written 19 months ago by ▴ 10
0
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4
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303
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How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 20 months ago by 58k • written 20 months ago by • 0
0
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2
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692
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DO.db is missing after repeated installations-ReactomePA-ClusterProfiler-DOSE
software error reactomePA DOSE DO.db there is no package called ‘DO.db’
updated 23 months ago by 25k • written 23 months ago by • 0
0
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0
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289
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ReactomePA only showing 1 result
ReactomePA
2.4 years ago ayang • 0
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1
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335
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ReactomePA and genelist
ReactomePA
updated 2.5 years ago by • 0 • written 2.5 years ago by ▴ 10
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0
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318
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viewPathway not showing a gene of interest
ReactomePA
2.7 years ago santos22903 • 0
2
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5
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1.3k
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How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 2.9 years ago by ★ 1.2k • written 2.9 years ago by ▴ 20
1
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2
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881
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ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
3.4 years ago martin.busch • 0
0
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5
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731
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
3.4 years ago martin.busch • 0
2
votes
4
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857
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 3.4 years ago by ★ 1.2k • written 3.4 years ago by • 0
0
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2
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868
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p-values in Reactome and ReactomePA
reactomepa reactome
updated 3.6 years ago by ★ 1.2k • written 3.6 years ago by • 0
3
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5
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866
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
3.6 years ago thomasjenner333 • 0
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2
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739
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Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 3.8 years ago by ★ 1.2k • written 3.8 years ago by • 0
0
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3
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857
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
3.8 years ago andrew.gehrke • 0
3
votes
2
replies
2.2k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 4.0 years ago by ★ 1.2k • written 4.0 years ago by ▴ 10
3
votes
4
replies
900
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 4.0 years ago by ▴ 150 • written 4.0 years ago by ▴ 10
3
votes
1
reply
594
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 4.3 years ago by ▴ 650 • written 4.3 years ago by • 0
0
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1
reply
758
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
4.4 years ago bhgyu ▴ 30
1
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8
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1.0k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
4.6 years ago juls • 0
1
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1
reply
834
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
4.8 years ago Kajus Baidžajevas ▴ 10
5
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4
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968
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 4.8 years ago by ▴ 100 • written 4.8 years ago by ▴ 20
0
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1
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815
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 5.1 years ago by 58k • written 5.1 years ago by • 0
1
vote
1
reply
951
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 5.1 years ago by ★ 1.2k • written 5.1 years ago by ▴ 10
4
votes
3
replies
992
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 5.2 years ago by ★ 1.2k • written 5.2 years ago by ▴ 580
0
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1
reply
822
views
ReactomePA - Change colors in barplot
reactomepa
updated 5.2 years ago by ★ 1.2k • written 5.2 years ago by ▴ 860
0
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14
replies
1.9k
views
Error in ReactomePA
r reactomepa
updated 5.3 years ago by ★ 1.2k • written 5.3 years ago by ▴ 20
1
vote
3
replies
1.6k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 6.0 years ago by ▴ 10 • written 6.1 years ago by ▴ 10
2
votes
4
replies
1.5k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 6.6 years ago by ★ 1.2k • written 6.6 years ago by ▴ 140
37 results • Page 1 of 1
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Replies
Comment: DESeq2 normalization when using with derfinder by Debayan ▴ 20
Thanks a lot for the clarification.
Comment: results() function and finding the difference of differences by Nayrouz • 0
That's a great idea. I was wondering if there is a way to form a 1-row matrix that has a -1 for the `genotypeII.conditionB` coefficient a…
Comment: ensembldb support for Ensembl's transcript_name column by Johannes Rainer ★ 1.9k
Hi Mike, the `EnsDb`s you get from e.g. `AnnotationHub` are not created from GTF files but from the Ensembl databases using the Ensembl Pe…
Answer: Interaction model genes don't intersect by Michael Love 34k
This is fine that the trends don’t intersect — that is not what interaction terms are used to detect. No we don’t have a test for inters…
Comment: How to add pseudocount to DESeq2 dds object by Michael Love 34k
If these questionable samples have 0s for genes where other samples have high counts, where do those samples have their counts? Maybe they …
Votes
Answer: DESeq2 normalization when using with derfinder
Answer: DESeq2 normalization when using with derfinder
Answer: mitochondrial RNA percentage in bulk RNAseq data
Answer: mitochondrial RNA percentage in bulk RNAseq data
Comment: How to add pseudocount to DESeq2 dds object
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