Showing : GSEa • reset
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311
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
28 days ago • updated 17 days ago Gordon • 0
2
votes
1
reply
180
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 26 days ago by ★ 3.9k • written 28 days ago by ▴ 10
4
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3
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204
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Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 4 weeks ago by • 0
0
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1
reply
556
views
choosing rank for GSEA
gsea DESeq2
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
0
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3
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1.2k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 5 months ago by • 0 • written 8 months ago by • 0
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0
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592
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using fgsea to compare two datasets
GSEA fgsea
9 months ago Cen • 0
1
vote
1
reply
935
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 9 months ago by 50k • written 9 months ago by • 0
7
votes
8
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11k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 12 months ago by ★ 4.0k • written 7.7 years ago by ▴ 20
2
votes
3
replies
902
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 15 months ago by ▴ 40 • written 15 months ago by • 0
0
votes
1
reply
590
views
GSA type of input data
GSEA GSA vst
updated 15 months ago by 41k • written 15 months ago by ▴ 30
0
votes
1
reply
790
views
DGE genes are not available in GSEA
dge gsea
updated 16 months ago by ★ 3.9k • written 16 months ago by • 0
7
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6
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2.1k
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Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 15 months ago by 50k • written 16 months ago by ▴ 30
2
votes
3
replies
896
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 17 months ago by • 0 • written 17 months ago by • 0
2
votes
4
replies
1.3k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 21 months ago by 50k • written 21 months ago by ▴ 10
0
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3
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1.8k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 17 months ago by ▴ 60 • written 21 months ago by • 0
0
votes
2
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3.2k
views
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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1.0k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.1 years ago by ★ 3.2k • written 2.1 years ago by ▴ 10
9
votes
13
replies
6.3k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 10 weeks ago by ★ 4.0k • written 2.1 years ago by ▴ 30
2
votes
1
reply
965
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
votes
2
replies
2.2k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.2 years ago Emilia ▴ 30
0
votes
1
reply
795
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.4 years ago lessismore ▴ 20
2
votes
1
reply
2.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.2k • written 3.8 years ago by ▴ 40
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.0 years ago by ★ 3.2k • written 4.0 years ago by ▴ 60
2
votes
2
replies
3.0k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by • 0
8
votes
5
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3.4k
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
votes
4
replies
2.4k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.3 years ago by • 0 • written 5.1 years ago by ▴ 40
0
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1
reply
800
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.1 years ago Diana ▴ 10
0
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1
reply
2.4k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.1 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 5.1 years ago by 41k • written 5.1 years ago by • 0
3
votes
3
replies
1.5k
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 5.3 years ago by 0 • written 5.4 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 5.4 years ago by ▴ 50 • written 5.4 years ago by ▴ 10
0
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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 5.5 years ago by 41k • written 5.5 years ago by • 0
0
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2
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1.6k
views
gene set enrichment analysis
GSEA GSA
updated 5.5 years ago by 50k • written 5.5 years ago by ▴ 670
0
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2
replies
1.2k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.6 years ago santos22903 • 0
5
votes
7
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2.5k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 5.7 years ago by 50k • written 5.7 years ago by ▴ 10
0
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0
replies
1.0k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
5.7 years ago l.brown ▴ 10
0
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3
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2.8k
views
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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1.7k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 5.8 years ago by 41k • written 5.8 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
5.8 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 6.0 years ago by 50k • written 6.0 years ago by ▴ 20
2
votes
2
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4.0k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.1 years ago by ★ 1.2k • written 6.1 years ago by • 0
1
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2
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2.3k
views
GSVA for single sample
gsea gsva ssgsea
6.2 years ago jaison75 ▴ 20
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2
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1.6k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
1
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1
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1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.3 years ago Stane ▴ 40
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0
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1.2k
views
GSEA-class file (.cls) parsing error message
gsea
6.3 years ago snguyen268 • 0
0
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1
reply
2.3k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.4 years ago giuseppe0525 • 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.4 years ago giuseppe0525 • 0
4
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1
reply
3.2k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.5 years ago by ▴ 240 • written 6.5 years ago by ▴ 30
0
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1
reply
1.1k
views
BioQC R package issue with broad gmt files
R BioQC gmt GSEA
6.5 years ago Seymoo • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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