Showing : reactomePA • reset
2
votes
3
replies
934
views
Why `FoldEnrichment`,`RichFactor`and `zScore` are not in the ReactomePA::enrichPathway result
DOSE ReactomePA
3 months ago Yifeii.Ge • 0
1
vote
2
replies
2.0k
views
ReactomePA:enrichPathway error in universe parameter
enrichPathway ReactomePA
updated 2.2 years ago by ▴ 40 • written 4.8 years ago by ▴ 10
4
votes
4
replies
5.3k
views
Clarifications on p-values in enrichResult objects
clusterProfiler reactomepa dose
updated 2.3 years ago by • 0 • written 8.5 years ago by ▴ 680
0
votes
0
replies
836
views
ReactomePA list of pathway plots
ReactomePA
2.7 years ago curiousmind007 ▴ 10
1
vote
1
reply
854
views
Meaning of brown-coloured nodes in the graph produced by the ReactomePA viewPathway() function.
clusterProfiler ReactomePA
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by ▴ 10
0
votes
1
reply
1.7k
views
How to download annotation package for oryza sativa Japonica and Oryza sativa indica for pathway analysis?
reactomePA package annotation
updated 3.1 years ago by 4.1k • written 3.1 years ago by ▴ 20
0
votes
0
replies
1.0k
views
enrichPathway error when checking condition lengths used
DOSE ReactomePA
4.0 years ago Lluís Revilla Sancho ▴ 760
3
votes
4
replies
3.1k
views
Download of package ‘reactome.db’ failed (Ubuntu, not for Windows)
reactome.db ReactomePA
4.0 years ago florianjt • 0
0
votes
0
replies
738
views
Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.3 years ago paun_bio • 0
0
votes
2
replies
1.6k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview ReactomePA
updated 4.7 years ago by 68k • written 4.7 years ago by • 0
0
votes
9
replies
2.1k
views
ReactomePA error graph
r rnaseq bulk GO ReactomePA
4.7 years ago camillab. ▴ 10
0
votes
0
replies
972
views
reactomePA error input file
r reactomePA enrichment
updated 4.7 years ago by ★ 4.0k • written 4.7 years ago by ▴ 10
0
votes
0
replies
1.2k
views
similarity coefficients used in emapplot {enrichplot} / gsePathway {ReactomePA} and simplify {clusterProfiler}
enrichplot ReactomePA clusterProfiler similarity coefficients emapplot
4.8 years ago jan.soderman • 0
0
votes
8
replies
3.0k
views
Adding Enrichresults for creating plot
ReactomePA clusterProfiler
4.8 years ago felix.thaler • 0
0
votes
1
reply
4.8k
views
How to modify label text size/line width in cnetplot (ReactomePA/clusterProfiler)
clusterProfiler ReactomePA
updated 4.9 years ago by ★ 1.2k • written 4.9 years ago by ▴ 10
0
votes
4
replies
2.4k
views
How to list all "..." parameters inside R function
ReactomePA clusterProfiler
updated 5.0 years ago by 68k • written 5.0 years ago by • 0
0
votes
2
replies
2.5k
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 5.2 years ago by 25k • written 5.2 years ago by • 0
0
votes
0
replies
914
views
ReactomePA only showing 1 result
ReactomePA
5.7 years ago ayang • 0
0
votes
1
reply
1.2k
views
ReactomePA and genelist
ReactomePA
updated 5.8 years ago by • 0 • written 5.8 years ago by ▴ 10
0
votes
0
replies
935
views
viewPathway not showing a gene of interest
ReactomePA
6.0 years ago santos22903 • 0
2
votes
5
replies
4.1k
views
How to convert data frame obtained with enrichPathway back to an enrichPathway result after editing/subsetting?
ReactomePA
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by ▴ 30
1
vote
2
replies
2.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.7 years ago martin.busch • 0
0
votes
5
replies
2.4k
views
ReactomePA / Reactome: Crash when plotting
reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome
6.7 years ago martin.busch • 0
2
votes
4
replies
2.7k
views
ReactomePA / Reactome: Extraction of genes within a term
pathways reactomepa functional annotation
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
0
votes
2
replies
2.5k
views
p-values in Reactome and ReactomePA
reactomepa reactome
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
3
votes
5
replies
2.5k
views
ReactomePA - Pathway analysis for DE porcine genes
reactomepa clusterprofiler
6.9 years ago thomasjenner333 • 0
0
votes
2
replies
1.9k
views
Reference for edge and node properties suitable for enrichMap{DOSE}
DOSE ReactomePA enrichMap enrichPathway
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by • 0
0
votes
3
replies
2.4k
views
custom background list for ReactomePA
reactomepa chipseeker Guangchuang Yu
7.1 years ago andrew.gehrke • 0
3
votes
2
replies
6.2k
views
Pathway analysis using ReactomePA::enrichPathway(): doubts about minGSSize and maxGSSize arguments
reactomepa pathway analysis enrichment analysis clusterprofiler
updated 7.3 years ago by ★ 1.2k • written 7.3 years ago by ▴ 10
3
votes
4
replies
2.3k
views
Enrichment Analysis for Shot-gun proteomics data using the ReactomePA package: problem with identities loss
reactomepa reactome.db reactome proteomics uniprot accessions
updated 7.3 years ago by ▴ 150 • written 7.3 years ago by ▴ 10
3
votes
1
reply
1.4k
views
ReactomePA enrichMap function - a question regarding the connections between nodes
reactomepa
updated 7.6 years ago by ▴ 760 • written 7.6 years ago by • 0
0
votes
1
reply
1.6k
views
GSEA threshold question
GSEa r clusterprofiler reactomepa
7.7 years ago bhgyu ▴ 30
1
vote
8
replies
2.7k
views
ReactomePA gsePathway - a couple of questions regarding the input and output
reactomepa
7.9 years ago juls • 0
1
vote
1
reply
1.8k
views
ReactomePA viewPathway DE node and legend colour
DOSE ReactomePA
8.1 years ago Kajus Baidžajevas ▴ 10
5
votes
4
replies
2.1k
views
Reactome pathways in ReactomeDB/graphite
reactomepa reactome graphite
updated 8.1 years ago by ▴ 100 • written 8.1 years ago by ▴ 40
0
votes
1
reply
1.5k
views
Dependent library issue when loading ReactomePA
ReactomePA
updated 8.4 years ago by 68k • written 8.4 years ago by • 0
1
vote
1
reply
1.7k
views
how to link ReactomePA with DESeq2
ReactomePA GO
updated 8.4 years ago by ★ 1.2k • written 8.4 years ago by ▴ 10
0
votes
1
reply
2.1k
views
ReactomePA - Change colors in barplot
reactomepa
updated 8.5 years ago by ★ 1.2k • written 8.5 years ago by ▴ 860
0
votes
14
replies
3.9k
views
Error in ReactomePA
r reactomepa
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by ▴ 20
1
vote
3
replies
3.8k
views
Reactome pathway analysis using ReactomePA
reactomepa R bioconductor ReactomePA
updated 9.4 years ago by ▴ 10 • written 9.4 years ago by ▴ 10
2
votes
4
replies
2.5k
views
ReactomePA : error with gsePathway
ReactomePA gsePathway
updated 9.9 years ago by ★ 1.2k • written 9.9 years ago by ▴ 140
41 results • Page 1 of 1
Recent ...
Replies
Comment: How to formulate 2 factor nested design in DESeq2 by Mariane • 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data by gaye.yilmaz • 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes by James W. MacDonald 68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2 by Marwan • 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
Answer: Differential variance analysis - can i use deseq2 by Michael Love 43k
We don't have a test of differential variance but other Bioconductor packages can, check similar posts (even on the right side bar) or use …
Votes
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Awards • All
Popular Question to user_bioinfo • 0
Scholar to Michael Love 43k
Popular Question to daniel.carbajo • 0
Popular Question to xiaofeiwang198266 • 0
Popular Question to maltethodberg ▴ 180
Locations • All
WEHI, Melbourne, Australia, 29 minutes ago
The city by the bay, 2 hours ago
India, 2 hours ago
United States, 2 hours ago
Australia, 3 hours ago
Traffic: 1105 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6