Showing : GeneSetEnrichment • reset
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fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea GeneSetEnrichment splines RNASeq
7 months ago GT • 0
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News: GSEA in R/Bioconductor course
GSEABenchmarkeR pairedGSEA GeneSetEnrichment
7 months ago info ▴ 10
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cameraPR() non directional test
CAMERA GeneSetEnrichment
8 months ago • updated 7 months ago Hugo Varet ▴ 80
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News: Gene Set Enrichment Analysis in Bioconductor course
GSEABase GeneSetEnrichment goseq
8 months ago • updated 7 months ago info ▴ 10
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Comparing Mock vs Infected in WT and Knockout Cells
DESeq2 DifferentialExpression DifferentialRegulation RNASeq GeneSetEnrichment
updated 8 months ago by 43k • written 8 months ago by • 0
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fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
13 months ago Assa Yeroslaviz ★ 1.5k
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How to rank DEG for GSEA using DEseq2 result ?
DESeq2 limma GeneSetEnrichment
updated 15 months ago by ★ 5.0k • written 15 months ago by • 0
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Gene set enrichment analysis
clusterProfiler GeneSetEnrichment
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
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geneList error in clusterprofiler
clusterProfiler GeneSetEnrichment
18 months ago Ana • 0
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1.0k
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How to make GSEAplot with chip set
geneset GeneSetEnrichment msigdb
18 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 19 months ago by • 0 • written 7.9 years ago by ▴ 20
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BubbleGUM for multi group comparison of gene set enrichment
RNASeqData GeneSetEnrichment multiGSEA
2.3 years ago sonal • 0
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2.1k
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How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO GeneSet clusterProfiler GeneSetEnrichment
updated 2.3 years ago by 68k • written 2.3 years 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
3.3 years ago Bhavana • 0
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enrichment to common gene
GeneSetEnrichment genes genetogo
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 20 months ago by ★ 5.0k • written 3.6 years ago by ▴ 70
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GSEA using clusterProfiler with non-model organism.
clusterProfiler KEGG GeneSetEnrichment
4.0 years ago makrez ▴ 10
3
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1.9k
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Self-contained gene set testing with DESeq2 results
roast DESeq2 GeneSetEnrichment
updated 4.8 years ago by 53k • written 4.8 years ago by • 0
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Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler GeneSetEnrichment enrichplot
updated 4.8 years ago by ▴ 40 • written 4.9 years ago by • 0
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Clusterprofiler - best practise for missing ids
ReactomePA clusterProfiler GeneSetEnrichment
4.9 years ago paun_bio • 0
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3.8k
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Problem retrieving graphics in clusterprofiler
software error clusterprofiler GO genesetenrichment
9.5 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 9.6 years ago by ★ 13k • written 9.6 years ago by ▴ 160
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News: Announcing the EnrichmentBrowser 2.0
genesetenrichment functional enrichment enrichmentbrowser News
9.7 years ago Ludwig Geistlinger ▴ 70
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6.0k
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Using goseq on non-model organism - how to define genome?
goseq go genesetenrichment
updated 9.8 years ago by 53k • written 9.8 years ago by ▴ 270
2
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1.3k
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elim method for KEGG pathways?
KEGG genesetenrichment elim
updated 9.9 years ago by 68k • written 9.9 years ago by ▴ 40
2
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2
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2.4k
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Goseq supported organism (felcat5) has an error when testing
goseq genesetenrichment annotation
updated 10.2 years ago by ▴ 320 • written 10.2 years ago by ▴ 20
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5.1k
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reactome.db is not updated?
genesetenrichment pathways reactome.db
updated 10.5 years ago by ▴ 150 • written 10.9 years ago by ★ 1.2k
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6.0k
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Reduce the redundancy of enriched GO terms
GO topgo genesetenrichment
updated 10.7 years ago by ★ 1.6k • written 10.7 years ago by ▴ 150
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Using segAnglePo() for a set of genes
geneexpression genesetenrichment segAnglePo
10.9 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
10.9 years ago Guangchuang Yu ★ 1.2k
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2.3k
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Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 70
31 results • Page 1 of 1
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry by teamardigen • 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
I am, but perhaps I'm not understanding how it should work. > sse = DropletUtils::read10xCounts(curr_files[1], mtx.class = 'SVT_Sparse…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Did you use the development version as Aaron suggested? There is an argument to read the market matrix file directly into an `SVT_SparseMat…
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Drug datasets for RNA-seq
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