Showing : genesetenrichment • reset
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
5 weeks ago GT • 0
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News: GSEA in R/Bioconductor course
GSEABenchmarkeR pairedGSEA GeneSetEnrichment
7 weeks ago info ▴ 10
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447
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cameraPR() non directional test
CAMERA GeneSetEnrichment
8 weeks ago Hugo Varet ▴ 80
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News: Gene Set Enrichment Analysis in Bioconductor course
GSEABase GeneSetEnrichment goseq
9 weeks ago • updated 7 weeks ago info ▴ 10
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 10 weeks ago by 43k • written 10 weeks ago by • 0
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fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
7 months ago Assa Yeroslaviz ★ 1.5k
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 9 months ago by ★ 4.8k • written 9 months ago by • 0
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Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 11 months ago by ★ 4.1k • written 11 months ago by • 0
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
12 months ago Ana • 0
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How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
12 months ago Seongsu • 0
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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 13 months ago by • 0 • written 7.4 years ago by ▴ 20
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
21 months ago sonal • 0
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How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 21 months ago by 68k • written 21 months 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
2.8 years ago Bhavana • 0
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enrichment to common gene
GeneSetEnrichment genes genetogo
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 14 months ago by ★ 4.8k • written 3.1 years ago by ▴ 70
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GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
3.5 years ago makrez ▴ 10
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1.7k
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Self-contained gene set testing with DESeq2 results
roast DESeq2 GeneSetEnrichment
updated 4.4 years ago by 52k • written 4.4 years ago by • 0
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Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler GeneSetEnrichment enrichplot
updated 4.3 years ago by ▴ 40 • written 4.4 years ago by • 0
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Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.4 years ago paun_bio • 0
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3.6k
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Problem retrieving graphics in clusterprofiler
software error clusterprofiler GO genesetenrichment
9.0 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 9.1 years ago by ★ 13k • written 9.1 years ago by ▴ 160
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News: Announcing the EnrichmentBrowser 2.0
genesetenrichment functional enrichment enrichmentbrowser News
9.2 years ago Ludwig Geistlinger ▴ 70
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5.7k
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Using goseq on non-model organism - how to define genome?
goseq go genesetenrichment
updated 9.4 years ago by 52k • written 9.4 years ago by ▴ 260
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1.3k
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elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 9.4 years ago by 68k • written 9.4 years ago by ▴ 40
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2.3k
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Goseq supported organism (felcat5) has an error when testing
goseq genesetenrichment annotation
updated 9.7 years ago by ▴ 320 • written 9.7 years ago by ▴ 20
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4.7k
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reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 10.1 years ago by ▴ 150 • written 10.4 years ago by ★ 1.2k
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5.8k
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Reduce the redundancy of enriched GO terms
GO topgo genesetenrichment
updated 10.2 years ago by ★ 1.6k • written 10.2 years ago by ▴ 150
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Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
10.4 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
10.4 years ago Guangchuang Yu ★ 1.2k
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 11.1 years ago by ★ 13k • written 11.1 years ago by ▴ 70
31 results • Page 1 of 1
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Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0
That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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