Showing : msigdb • reset
2
votes
2
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1.3k
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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
0
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0
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610
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Filtering the genesets for fgseaMultiLevel
msigdb fgsea msig
19 months ago Tanvi • 0
0
votes
2
replies
1.1k
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How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
21 months ago Seongsu • 0
4
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3
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1.4k
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Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 22 months ago by • 0
4
votes
4
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5.6k
views
How should I run ssGSEA Hallmark Enrichment Analysis?
ssgsea GSVA biotype proteincoding msigdb
updated 15 months ago by • 0 • written 2.1 years ago by ▴ 200
1
vote
1
reply
2.6k
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Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 3.8 years ago by ★ 3.4k • written 3.8 years ago by • 0
1
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1
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2.7k
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Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 7.6 years ago by ▴ 170
2
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2
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5.6k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by • 0
1
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2
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1.8k
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Update to MSigDB derivates for romer()?
limma romer msigdb
updated 10.4 years ago by 68k • written 10.4 years ago by ▴ 40
0
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0
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1.7k
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hyperGTest for MSigDB categories
category gostats msigdb hypergeometric test
10.5 years ago petyuk ▴ 70
10 results • Page 1 of 1
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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.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
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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