Showing : GSEA • reset
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
8 weeks ago • updated 6 weeks ago Gordon • 0
2
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1
reply
233
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 7 weeks ago by ★ 4.0k • written 8 weeks ago by ▴ 10
4
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3
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257
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Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 8 weeks ago by • 0
0
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1
reply
658
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choosing rank for GSEA
gsea DESeq2
updated 7 months ago by ★ 4.1k • written 7 months ago by • 0
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3
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1.4k
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gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 6 months ago by • 0 • written 9 months ago by • 0
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640
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using fgsea to compare two datasets
GSEA fgsea
10 months ago Cen • 0
1
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1
reply
1.0k
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How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 10 months ago by 50k • written 10 months ago by • 0
7
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8
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11k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 12 months ago by ★ 4.1k • written 7.8 years ago by ▴ 20
2
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3
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956
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GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 16 months ago by ▴ 40 • written 16 months ago by • 0
0
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1
reply
611
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GSA type of input data
GSEA GSA vst
updated 16 months ago by 42k • written 16 months ago by ▴ 30
0
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1
reply
835
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DGE genes are not available in GSEA
dge gsea
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
7
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6
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2.2k
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Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 16 months ago by 50k • written 17 months ago by ▴ 30
2
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3
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925
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 18 months ago by • 0 • written 18 months ago by • 0
2
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4
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1.4k
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pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 22 months ago by 50k • written 22 months ago by ▴ 10
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3
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2.0k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 18 months ago by ▴ 60 • written 22 months ago by • 0
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2
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3.4k
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What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
23 months ago • updated 22 months ago Bhavana • 0
0
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1
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1.1k
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GSEA using custom GO annotations
RNASeq GSEA
updated 2.2 years ago by ★ 3.3k • written 2.2 years ago by ▴ 10
9
votes
13
replies
6.8k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.1k • written 2.2 years ago by ▴ 30
2
votes
1
reply
987
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
0
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2
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2.3k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.3 years ago Emilia ▴ 30
0
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1
reply
825
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.5 years ago lessismore ▴ 20
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 50
7
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11
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2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.1 years ago by ★ 3.3k • written 4.1 years ago by ▴ 60
2
votes
2
replies
3.2k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 4.9 years ago by ▴ 70 • written 4.9 years ago by • 0
8
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5
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3.5k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 110
2
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4
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2.5k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.4 years ago by • 0 • written 5.2 years ago by ▴ 40
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1
reply
825
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.2 years ago Diana ▴ 10
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1
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2.5k
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Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.2 years ago aboumarshal • 0
3
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7
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26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
3
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3
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1.6k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 50
0
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3
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1.3k
views
gseaplot vertical line
clusterProfiler gsea
updated 5.4 years ago by 0 • written 5.5 years ago by • 0
0
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2
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1.3k
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GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 5.5 years ago by ▴ 50 • written 5.5 years ago by ▴ 10
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1
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1.2k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 5.6 years ago by 42k • written 5.6 years ago by • 0
0
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2
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1.6k
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gene set enrichment analysis
GSEA GSA
updated 5.6 years ago by 50k • written 5.6 years ago by ▴ 670
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2
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1.2k
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Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.7 years ago santos22903 • 0
5
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7
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2.6k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 10
0
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0
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1.1k
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Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
5.8 years ago l.brown ▴ 10
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3
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2.9k
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fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
5.8 years ago atakanekiz ▴ 30
0
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3
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1.8k
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Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 5.9 years ago by 42k • written 5.9 years ago by • 0
1
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2
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1.8k
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ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.9 years ago martin.busch • 0
1
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1
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1.4k
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Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.1 years ago by 50k • written 6.1 years ago by ▴ 20
2
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2
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4.1k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
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2
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2.4k
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GSVA for single sample
gsea gsva ssgsea
6.3 years ago jaison75 ▴ 20
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2
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1.7k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by • 0
1
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1
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1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.4 years ago Stane ▴ 40
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0
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1.3k
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GSEA-class file (.cls) parsing error message
gsea
6.4 years ago snguyen268 • 0
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1
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2.4k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.5 years ago giuseppe0525 • 0
2
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6
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12k
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GSEA using clusterProfiler
GSEA clusterProfiler
6.5 years ago giuseppe0525 • 0
4
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1
reply
3.3k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.6 years ago by ▴ 260 • written 6.6 years ago by ▴ 30
0
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1
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1.1k
views
BioQC R package issue with broad gmt files
R BioQC gmt GSEA
6.6 years ago Seymoo • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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