Showing : genesetenrichment • reset
8
votes
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
9
votes
13
replies
6.4k
views
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
5
votes
7
replies
4.9k
views
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
1
vote
4
replies
3.0k
views
Problem retrieving graphics in clusterprofiler
software error clusterprofiler GO genesetenrichment
8.0 years ago José Luis Lavín ▴ 10
4
votes
4
replies
3.7k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler GO GO enrichment genesetenrichment
updated 5 weeks ago by • 0 • written 6.4 years ago by ▴ 20
0
votes
3
replies
1.8k
views
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
2
votes
2
replies
2.0k
views
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
0
votes
2
replies
164
views
How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
24 days ago • updated 23 days ago Seongsu • 0
3
votes
2
replies
1.2k
views
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
1
vote
2
replies
110
views
geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
8 days ago Ana • 0
0
votes
2
replies
3.2k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
22 months ago Bhavana • 0
0
votes
1
reply
779
views
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
2
votes
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
1
vote
1
reply
5.2k
views
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
0
votes
1
reply
1.4k
views
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
votes
1
reply
861
views
enrichment to common gene
GeneSetEnrichment genes genetogo
updated 22 months ago by ▴ 780 • written 22 months ago by • 0
1
vote
0
replies
1.3k
views
News: Announcing the EnrichmentBrowser 2.0
genesetenrichment functional enrichment enrichmentbrowser News
8.2 years ago Ludwig Geistlinger ▴ 70
0
votes
0
replies
1.7k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
9.4 years ago Guangchuang Yu ★ 1.2k
1
vote
0
replies
1.1k
views
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
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
0
votes
0
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1.1k
views
Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
9.4 years ago Peter.Wood • 0
0
votes
0
replies
321
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
9 months ago sonal • 0
1
vote
0
replies
1.3k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
2.5 years ago makrez ▴ 10
23 results • Page 1 of 1
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Replies
Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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