Showing : GeneSetEnrichment • reset
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News: GSEA in R/Bioconductor course
GSEABenchmarkeR pairedGSEA GeneSetEnrichment
written 10 months ago by ▴ 10
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550
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
10 months ago GT • 0
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2
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720
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cameraPR() non directional test
CAMERA GeneSetEnrichment
10 months ago Hugo Varet ▴ 80
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860
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News: Gene Set Enrichment Analysis in Bioconductor course
GSEABase GeneSetEnrichment goseq
11 months ago • updated 10 months ago info ▴ 10
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465
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 11 months ago by 43k • written 11 months ago by • 0
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fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
16 months ago Assa Yeroslaviz ★ 1.5k
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 18 months ago by ★ 5.0k • written 18 months ago by • 0
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1.7k
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Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 20 months ago by ★ 4.1k • written 20 months ago by • 0
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2.8k
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
21 months ago Ana • 0
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1.1k
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How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
21 months ago Seongsu • 0
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5.4k
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Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 22 months ago by • 0 • written 8.1 years ago by ▴ 20
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873
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
2.5 years ago sonal • 0
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2.3k
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How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 2.5 years ago by 68k • written 2.5 years ago by • 0
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What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
3.6 years ago Bhavana • 0
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enrichment to common gene
GeneSetEnrichment genes genetogo
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 23 months ago by ★ 5.0k • written 3.8 years ago by ▴ 70
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2.2k
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GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
4.2 years ago makrez ▴ 10
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2.1k
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Self-contained gene set testing with DESeq2 results
roast DESeq2 GeneSetEnrichment
updated 5.1 years ago by 53k • written 5.1 years ago by • 0
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1.9k
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Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler GeneSetEnrichment enrichplot
updated 5.0 years ago by ▴ 40 • written 5.1 years ago by • 0
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Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
5.2 years ago paun_bio • 0
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3.9k
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Problem retrieving graphics in clusterprofiler
software error clusterprofiler GO genesetenrichment
9.7 years ago José Luis Lavín ▴ 10
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performance of limma gene set analysis in relation to Tarca et al. (2013)
limma genesetenrichment
updated 9.9 years ago by ★ 13k • written 9.9 years ago by ▴ 160
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News: Announcing the EnrichmentBrowser 2.0
genesetenrichment functional enrichment enrichmentbrowser News
10.0 years ago Ludwig Geistlinger ▴ 80
5
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6.1k
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Using goseq on non-model organism - how to define genome?
goseq go genesetenrichment
updated 10.1 years ago by 53k • written 10.1 years ago by ▴ 270
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1.4k
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elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 10.2 years ago by 68k • written 10.2 years ago by ▴ 40
2
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2
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2.5k
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Goseq supported organism (felcat5) has an error when testing
goseq genesetenrichment annotation
updated 10.4 years ago by ▴ 320 • written 10.4 years ago by ▴ 20
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5.3k
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reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 10.8 years ago by ▴ 150 • written 11.2 years ago by ★ 1.2k
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6.2k
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Reduce the redundancy of enriched GO terms
GO topgo genesetenrichment
updated 11.0 years ago by ★ 1.6k • written 11.0 years ago by ▴ 150
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Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
11.1 years ago Peter.Wood • 0
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2.1k
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
11.2 years ago Guangchuang Yu ★ 1.2k
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ▴ 70
31 results • Page 1 of 1
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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