Showing : GeneSetEnrichment • reset
1
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
9 days ago Ana • 0
0
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2
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167
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How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
25 days ago • updated 24 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 5 weeks ago by • 0 • written 6.4 years ago by ▴ 20
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0
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323
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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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784
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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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864
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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
1
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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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559
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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
views
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
1
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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
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
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
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
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
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
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1.1k
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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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Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona • 0
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
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