Showing : GeneSetEnrichment • reset
1
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
8 days ago Ana • 0
0
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2
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163
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How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
23 days ago • updated 22 days ago Seongsu • 0
4
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4
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3.7k
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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 4 weeks ago by • 0 • written 6.4 years ago by ▴ 20
0
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0
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321
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
9 months ago sonal • 0
0
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1
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776
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How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 9 months ago by 65k • written 9 months ago by • 0
0
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2
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3.2k
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What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
22 months ago Bhavana • 0
0
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1
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857
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enrichment to common gene
GeneSetEnrichment genes genetogo
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
9
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13
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6.4k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 weeks ago by ★ 4.0k • written 2.1 years ago by ▴ 30
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0
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1.3k
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GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.5 years ago makrez ▴ 10
3
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2
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1.2k
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Self-contained gene set testing with DESeq2 results
roast DESeq2 GeneSetEnrichment
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
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1
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1.4k
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Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler GeneSetEnrichment enrichplot
updated 3.3 years ago by ▴ 30 • written 3.4 years ago by • 0
0
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0
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557
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Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
3.4 years ago paun_bio • 0
1
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4
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3.0k
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Problem retrieving graphics in clusterprofiler
software error clusterprofiler GO genesetenrichment
8.0 years ago José Luis Lavín ▴ 10
1
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0
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1.1k
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performance of limma gene set analysis in relation to Tarca et al. (2013)
limma genesetenrichment
updated 8.1 years ago by ★ 13k • written 8.1 years ago by ▴ 160
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0
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1.3k
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News: Announcing the EnrichmentBrowser 2.0
genesetenrichment functional enrichment enrichmentbrowser News
8.2 years ago Ludwig Geistlinger ▴ 70
5
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7
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4.9k
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Using goseq on non-model organism - how to define genome?
goseq go genesetenrichment
updated 8.4 years ago by 50k • written 8.4 years ago by ▴ 250
2
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1
reply
1.0k
views
elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 8.4 years ago by 65k • written 8.4 years ago by ▴ 40
2
votes
2
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2.0k
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Goseq supported organism (felcat5) has an error when testing
goseq genesetenrichment annotation
updated 8.7 years ago by ▴ 310 • written 8.7 years ago by ▴ 20
8
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14
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3.8k
views
reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 9.1 years ago by ▴ 150 • written 9.4 years ago by ★ 1.2k
1
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1
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5.2k
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Reduce the redundancy of enriched GO terms
GO topgo genesetenrichment
updated 9.2 years ago by ★ 1.6k • written 9.2 years ago by ▴ 150
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Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
9.4 years ago Peter.Wood • 0
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0
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1.7k
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
9.4 years ago Guangchuang Yu ★ 1.2k
0
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3
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1.8k
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 10.1 years ago by ★ 13k • written 10.1 years ago by ▴ 70
23 results • Page 1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
C: when to apply quantile normalization with voom in limma/voom framework with RNA-
A: How to know if I should use voomWithQualityWeights() or not?
A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom
Answer: Log-cpm values from limma
Answer: Log-cpm values from limma
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