Showing : ReactomePA • reset
1
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2
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ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 16 months ago by ▴ 40 • written 4.0 years ago by ▴ 10
4
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4
replies
4.1k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 18 months ago by • 0 • written 7.6 years ago by ▴ 660
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0
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597
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ReactomePA list of pathway plots
ReactomePA
22 months ago curiousmind007 ▴ 10
1
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1
reply
622
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 24 months ago by ▴ 770 • written 24 months ago by ▴ 10
0
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1
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1.2k
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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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828
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
3.2 years ago Lluís Revilla Sancho ▴ 730
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4
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2.3k
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Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
3.2 years ago florianjt • 0
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0
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554
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Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
3.4 years ago paun_bio • 0
0
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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 3.8 years ago by • 0
0
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9
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1.5k
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ReactomePA error graph
r rnaseq bulk GO ReactomePA
3.8 years ago camillab. ▴ 10
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0
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754
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reactomePA error input file
r reactomePA enrichment
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
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0
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935
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
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8
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2.5k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.0 years ago felix.thaler • 0
0
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1
reply
3.9k
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
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4
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1.2k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
0
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2
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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
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0
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754
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ReactomePA only showing 1 result
ReactomePA
4.9 years ago ayang • 0
0
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1
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918
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ReactomePA and genelist
ReactomePA
updated 5.0 years ago by • 0 • written 5.0 years ago by ▴ 10
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0
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779
views
viewPathway not showing a gene of interest
ReactomePA
5.2 years ago santos22903 • 0
2
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5
replies
3.3k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 5.3 years ago by ★ 1.2k • written 5.4 years ago by ▴ 30
1
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2
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1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.8 years ago martin.busch • 0
0
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5
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1.9k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
5.9 years ago martin.busch • 0
2
votes
4
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2.1k
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
0
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2
replies
1.9k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
3
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5
replies
1.9k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.1 years ago thomasjenner333 • 0
0
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2
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1.5k
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Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
0
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3
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1.9k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
6.3 years ago andrew.gehrke • 0
3
votes
2
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4.7k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by ▴ 10
3
votes
4
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1.8k
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
0
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1
reply
1.3k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
6.9 years ago bhgyu ▴ 30
1
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8
replies
2.2k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.1 years ago juls • 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
5
votes
4
replies
1.8k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 7.3 years ago by ▴ 100 • written 7.3 years ago by ▴ 30
0
votes
1
reply
1.3k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 7.5 years ago by 65k • written 7.5 years ago by • 0
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
0
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1
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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
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14
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3.3k
views
Error in ReactomePA
r reactomepa
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by ▴ 20
1
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3
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3.0k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 8.5 years ago by ▴ 10 • written 8.5 years ago by ▴ 10
2
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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
40 results • Page 1 of 1
Recent ...
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Answer: OrgDb for maize by James W. MacDonald 65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR? by i.atanasoai • 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts by Michael Love 41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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