Showing : gene set enrichment • reset
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PLAGE method fails in GSVA if an overlap between gene sets and genes in expressions is less than two
gsva plage differential expression gene set enrichment
6.4 years ago krassowski.michal ▴ 40
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2
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Removing redundancy in Reactome pathways after performing gene set analysis with camera
camera limma gene set analysis gene set enrichment
updated 6.5 years ago by 52k • written 6.5 years ago by • 0
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1.3k
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Visualise gene set analysis plot
gene set analysis gene set enrichment limma
updated 6.7 years ago by 52k • written 6.7 years ago by • 0
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1
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1.5k
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Gene Set Enrichment based on gene presence/absence
gene set enrichment KEGG
updated 7.2 years ago by ▴ 760 • written 7.2 years ago by ▴ 10
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3
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2.2k
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Barcodeplot limma function using two logFC lists
limma edger barcodeplot gene set enrichment mroast
updated 7.3 years ago by 52k • written 7.3 years ago by • 0
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4
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3.6k
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No annotated genes found in universe error using goana and kegga
limma goana gene set enrichment
7.5 years ago emy_66 • 0
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4.4k
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enrichGO from DOSE, clusterprofiler is returning empty result.
DOSE clusterprofiler annotation gene ontology gene set enrichment
updated 7.5 years ago by ★ 1.2k • written 7.5 years ago by ▴ 20
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1
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1.5k
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News: Interested in developing a new gene set enrichment tool ?
gene ontology go analysis gene set enrichment gene set analysis News
updated 7.8 years ago by 25k • written 7.8 years ago by • 0
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3.0k
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Camera gene set interpretation
limma camera gene set analysis gene set enrichment
updated 8.3 years ago by 52k • written 8.3 years ago by • 0
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2
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3.1k
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topGO for Gene Ontology and Gene Set enrichment
topgo gene ontology gene set enrichment rna-seq bioinformatics
updated 8.3 years ago by ▴ 760 • written 8.6 years ago by ▴ 10
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3
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2.8k
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Gene Ontology and Gene Set Enrichment
rna-seq bioinformatics gene ontology gene set enrichment go
updated 8.6 years ago by ★ 1.2k • written 8.6 years ago by ▴ 10
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Comment: parameters of filterByExpr by caroline.zanchi ▴ 10
It worked, I think I finally understand and accept that fact. Sorry and thank you again !
Comment: parameters of filterByExpr by Gordon Smyth 52k
You seem to be coming back to the same fixed (but incorrect) idea of what filterByExpr() should be doing. I have tried to explain that filt…
Answer: edgeR in DMR mode - replicates give batch effect - how to build design matrix wi by Gordon Smyth 52k
modelMatrixMeth() works correctly. The second replicate factor has not been lost. Please do not make ad hoc manual modifications to the de…
Comment: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm by James W. MacDonald 68k
Probably not. Any given gene may be appended with many different GO terms, so you would end up with something that is not very useful. ``…
Comment: Heatmap of rnaseq data with z-score scale by James W. MacDonald 68k
`heatmap.2` is a CRAN package, and that's the relevant issue for this plot. It's got nothing to do with `DESeq2` or any other Bioconductor …
Votes
Answer: LogFC values in edgeR - w/wo intercept
How to formulate 2 factor nested design in DESeq2
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Answer: Adding gene names as row annotations to an RNAseq heatmap made with ComplexHeatm
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
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