Showing : Gsea • reset
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Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 10 weeks ago by 67k • written 10 weeks ago by • 0
1
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2
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1.2k
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How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 4 months ago by • 0
0
votes
1
reply
522
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Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 4 months ago by ★ 1.0k • written 4 months ago by • 0
1
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4
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806
views
Error in gseDO function
DOSE gsea
7 months ago Javier • 0
0
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2
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1.1k
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
9 months ago Gordon • 0
2
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2
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805
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 9 months ago by ▴ 10
4
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3
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712
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 9 months ago by • 0
0
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1
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1.4k
views
choosing rank for GSEA
gsea DESeq2
updated 14 months ago by ★ 4.6k • written 14 months ago by • 0
0
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3
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2.2k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 14 months ago by • 0 • written 17 months ago by • 0
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0
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925
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using fgsea to compare two datasets
GSEA fgsea
17 months ago Cen • 0
1
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1
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1.6k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 18 months ago by 52k • written 18 months ago by • 0
8
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8
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14k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 20 months ago by ★ 4.6k • written 8.4 years ago by ▴ 20
2
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3
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1.5k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 24 months ago by ▴ 40 • written 24 months ago by • 0
0
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1
reply
783
views
GSA type of input data
GSEA GSA vst
updated 2.0 years ago by 43k • written 2.0 years ago by ▴ 70
0
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1
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1.2k
views
DGE genes are not available in GSEA
dge gsea
updated 2.1 years ago by ★ 4.1k • written 2.1 years ago by • 0
7
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6
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3.2k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 2.0 years ago by 52k • written 2.1 years ago by ▴ 70
2
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3
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1.3k
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 2.2 years ago by • 0 • written 2.2 years ago by • 0
2
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4
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1.7k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.4 years ago by 52k • written 2.5 years ago by ▴ 10
0
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3
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2.8k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.2 years ago by ▴ 60 • written 2.5 years ago by • 0
0
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2
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4.9k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.5 years ago Bhavana • 0
0
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1
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1.8k
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GSEA using custom GO annotations
RNASeq GSEA
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by ▴ 10
12
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13
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9.7k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 months ago by ★ 4.6k • written 2.8 years ago by ▴ 70
2
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1
reply
1.2k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
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2
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3.2k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.9 years ago Emilia ▴ 40
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1
reply
1.0k
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
4.1 years ago lessismore ▴ 20
2
votes
1
reply
2.7k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.5 years ago by ★ 3.4k • written 4.5 years ago by ▴ 50
7
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11
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3.2k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 60
2
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2
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4.1k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.5 years ago by ▴ 70 • written 5.5 years ago by • 0
8
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5
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4.3k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.7 years ago by 52k • written 5.7 years ago by ▴ 120
2
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4
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3.0k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 4.0 years ago by • 0 • written 5.8 years ago by ▴ 40
0
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1
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1.0k
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.8 years ago Diana ▴ 10
0
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1
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3.3k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.8 years ago aboumarshal • 0
3
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7
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28k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
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3
replies
2.1k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.9 years ago by ★ 3.0k • written 5.9 years ago by ▴ 60
0
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3
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1.6k
views
gseaplot vertical line
clusterProfiler gsea
updated 6.0 years ago by 0 • written 6.1 years ago by • 0
0
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2
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1.7k
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 6.2 years ago by ▴ 50 • written 6.2 years ago by ▴ 10
0
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1
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1.4k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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2
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1.9k
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gene set enrichment analysis
GSEA GSA
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 670
0
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2
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1.5k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.3 years ago santos22903 • 0
5
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7
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3.5k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 6.4 years ago by 52k • written 6.4 years ago by ▴ 10
0
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0
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1.2k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
6.4 years ago l.brown ▴ 10
0
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3
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3.6k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
6.5 years ago atakanekiz ▴ 30
0
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3
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2.0k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
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2
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2.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.5 years ago martin.busch • 0
1
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1
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1.6k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 20
2
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2
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4.7k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
1
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2
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2.7k
views
GSVA for single sample
gsea gsva ssgsea
6.9 years ago jaison75 ▴ 20
0
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2
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2.1k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
1
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1
reply
2.2k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
7.0 years ago Stane ▴ 40
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0
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1.5k
views
GSEA-class file (.cls) parsing error message
gsea
7.0 years ago snguyen268 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: PCA of different bacterial species by Jeremy • 0
Your approach of using ~2500 single-copy orthologs and normalizing with VST or rlog for PCA is valid for exploring general clustering [pap…
Comment: RnBeads::combine() - error? by Urotree • 0
pheno <- rnb.set.arrays@pheno # Phenotypic data sites <- rnb.set.arrays@sites # CpG site definitions (data.frame) meth <- rnb.set…
Comment: RnBeads::combine() - error? by Urotree • 0
![enter image description here][1] [1]: /media/images/40d9778d-b044-4405-9b3d-2ba835f6 Hi, after I convert to RnBiseqSet, it shows "All…
Comment: RnBeads::combine() - error? by Urotree • 0
rnb.set.biseq <- RnBiseqSet( pheno = pheno, sites = sites, meth = meth, covg = NULL, # This can be NULL if coverage …
Answer: How to increase font for gene name and increase arrow size for GVIZ's ( UcscTra by ming • 0
`fontsize` for title font size, `fontsize.group` for gene symbol font size tx.track <- GeneRegionTrack(hg38.gtf, …
Votes
A: Full length single-cell RNA-seq - tximport output for downstream analysis
Answer: Understanding tximport working with salmon outputs
Answer: enrichGOgradient color change
How do I fix an odd voom plot in a combined dataset?
Answer: Warning message when running limma with covariates
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