Showing : GeneSetEnrichment • reset
8
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14
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3.8k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 9.0 years ago by ▴ 150 • written 9.4 years ago by ★ 1.2k
9
votes
13
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6.3k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 10 weeks ago by ★ 4.0k • written 2.1 years ago by ▴ 30
5
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7
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4.8k
views
Using goseq on non-model organism - how to define genome?
goseq go genesetenrichment
updated 8.3 years ago by 50k • written 8.3 years ago by ▴ 250
1
vote
4
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3.0k
views
Problem retrieving graphics in clusterprofiler
software error clusterprofiler GO genesetenrichment
8.0 years ago José Luis Lavín ▴ 10
4
votes
4
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3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 29 days ago by • 0 • written 6.3 years ago by ▴ 20
0
votes
3
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1.8k
views
Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 70
2
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2
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2.0k
views
Goseq supported organism (felcat5) has an error when testing
goseq genesetenrichment annotation
updated 8.7 years ago by ▴ 310 • written 8.7 years ago by ▴ 20
0
votes
2
replies
153
views
How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
18 days ago • updated 17 days ago Seongsu • 0
3
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2
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1.2k
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Self-contained gene set testing with DESeq2 results
roast DESeq2 GeneSetEnrichment
updated 3.3 years ago by 50k • written 3.3 years ago by • 0
1
vote
2
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78
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
2 days ago Ana • 0
0
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2
replies
3.2k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
22 months ago • updated 21 months ago Bhavana • 0
0
votes
1
reply
748
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 9 months ago by 65k • written 9 months ago by • 0
2
votes
1
reply
1.0k
views
elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 40
1
vote
1
reply
5.2k
views
Reduce the redundancy of enriched GO terms
GO topgo genesetenrichment
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 150
0
votes
1
reply
1.4k
views
Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler GeneSetEnrichment enrichplot
updated 3.3 years ago by ▴ 30 • written 3.4 years ago by • 0
0
votes
1
reply
844
views
enrichment to common gene
GeneSetEnrichment genes genetogo
updated 22 months ago by ▴ 770 • written 22 months ago by • 0
1
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0
replies
1.3k
views
News: Announcing the EnrichmentBrowser 2.0
genesetenrichment functional enrichment enrichmentbrowser News
8.2 years ago Ludwig Geistlinger ▴ 70
0
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0
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1.7k
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
9.4 years ago Guangchuang Yu ★ 1.2k
1
vote
0
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1.1k
views
performance of limma gene set analysis in relation to Tarca et al. (2013)
limma genesetenrichment
updated 8.1 years ago by ★ 13k • written 8.1 years ago by ▴ 160
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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0
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1.1k
views
Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
9.3 years ago Peter.Wood • 0
0
votes
0
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313
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
9 months ago sonal • 0
1
vote
0
replies
1.3k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.5 years ago makrez ▴ 10
23 results • Page 1 of 1
Recent ...
Replies
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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