Showing : GSEA • reset
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40
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Error in gseDO function
DOSE gsea
updated 14 hours ago by ★ 4.0k • written 14 hours ago by • 0
0
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2
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388
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
9 weeks ago • updated 7 weeks ago Gordon • 0
2
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1
reply
252
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 9 weeks ago by ★ 4.0k • written 9 weeks ago by ▴ 10
4
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3
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276
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Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 10 weeks ago by • 0
0
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1
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696
views
choosing rank for GSEA
gsea DESeq2
updated 7 months ago by ★ 4.2k • written 7 months ago by • 0
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 7 months ago by • 0 • written 9 months ago by • 0
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0
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654
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using fgsea to compare two datasets
GSEA fgsea
10 months ago Cen • 0
1
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1
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1.0k
views
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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12k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 13 months ago by ★ 4.2k • written 7.8 years ago by ▴ 20
2
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3
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973
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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
612
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GSA type of input data
GSEA GSA vst
updated 17 months ago by 42k • written 17 months ago by ▴ 40
0
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1
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847
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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 17 months ago by 50k • written 17 months ago by ▴ 40
2
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3
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933
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system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 19 months ago by • 0 • written 19 months ago by • 0
2
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4
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1.4k
views
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
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Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 19 months ago by ▴ 60 • written 23 months ago by • 0
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2
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3.4k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
23 months ago Bhavana • 0
0
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1
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1.1k
views
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
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6.9k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.2k • written 2.2 years ago by ▴ 40
2
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1
reply
991
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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2.4k
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
833
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.5 years ago lessismore ▴ 20
2
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1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.9 years ago by ★ 3.3k • written 3.9 years ago by ▴ 50
7
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11
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2.5k
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
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2
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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
votes
5
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3.6k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.1 years ago by 50k • written 5.1 years ago by ▴ 110
2
votes
4
replies
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
0
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1
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830
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.2 years ago Diana ▴ 10
0
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1
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2.6k
views
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
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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
replies
1.6k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.3 years ago by ★ 3.0k • written 5.3 years ago by ▴ 60
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
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 5.6 years ago by ▴ 50 • written 5.6 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
0
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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
votes
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
5.9 years ago atakanekiz ▴ 30
0
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3
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1.8k
views
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
views
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
views
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
1
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2
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2.4k
views
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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1.9k
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
views
GSEA-class file (.cls) parsing error message
gsea
6.4 years ago snguyen268 • 0
0
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1
reply
2.4k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.5 years ago giuseppe0525 • 0
2
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6
replies
12k
views
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
50 results • Page 1 of 1
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Comment: Cannot install oligo on Fedora by mbassal • 0
so whats the solution for this error?
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
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