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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558
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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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724
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cameraPR() non directional test
CAMERA GeneSetEnrichment
11 months ago • updated 10 months ago Hugo Varet ▴ 80
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870
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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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469
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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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1.2k
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How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
21 months ago Seongsu • 0
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5.5k
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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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874
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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 3.9 years ago by ▴ 70
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GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
4.2 years ago makrez ▴ 10
3
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2
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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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2.0k
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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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4
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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
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6.2k
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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
2
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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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14
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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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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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2.4k
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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
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by ATpoint ★ 5.0k
Yes, still it's not reproducible, yet hard to debug. I cannot reproduce myself either.
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening using pre-existing size factors estimating dispersions gene-wise dispersion estimates: 15 workers mean-dis…
Answer: BiocParallel (and DESeq2) - wrong args for environment subassignment by Benjamin • 0
Still happening in a clean install
Comment: limpa analysis advice by Gordon Smyth 53k
Yes, we use Astral currently. The main dataset in the limpa preprint is Astral. I don't see any major problems with your data and I think …
Comment: limpa analysis advice by SamGG ▴ 360
Thank you for your comments. Please note that I did not apply any filtering to the peptide intensity. The experimental protocol includes tw…
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Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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