Showing : GSEa • reset
0
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363
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
6 weeks ago • updated 5 weeks ago Gordon • 0
2
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1
reply
217
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 6 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
4
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3
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239
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Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 7 weeks ago by • 0
0
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1
reply
621
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choosing rank for GSEA
gsea DESeq2
updated 6 months ago by ★ 4.1k • written 6 months ago by • 0
0
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3
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1.3k
views
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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0
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627
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using fgsea to compare two datasets
GSEA fgsea
9 months ago Cen • 0
1
vote
1
reply
993
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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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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948
views
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
605
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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
votes
1
reply
817
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DGE genes are not available in GSEA
dge gsea
updated 17 months ago by ★ 3.9k • 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
votes
3
replies
919
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 18 months ago by • 0 • written 18 months ago by • 0
2
votes
4
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1.4k
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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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1.9k
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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3.3k
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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1.1k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.1 years ago by ★ 3.3k • written 2.1 years ago by ▴ 10
9
votes
13
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6.6k
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
981
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 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
818
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.4 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 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 40
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 4.0 years ago by ★ 3.3k • written 4.0 years ago by ▴ 60
2
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2
replies
3.1k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 4.8 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
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 5.2 years ago by ▴ 40
0
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1
reply
818
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
reply
2.5k
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
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
votes
3
replies
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
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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 5.5 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 5.5 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 5.5 years ago by 42k • written 5.6 years ago by • 0
0
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2
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1.6k
views
gene set enrichment analysis
GSEA GSA
updated 5.6 years ago by 50k • written 5.6 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
5.7 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 5.7 years ago by 50k • written 5.7 years ago by ▴ 10
0
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0
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1.0k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
5.8 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
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
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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
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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4.1k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.1 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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1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.3 years ago Stane ▴ 40
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0
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1.3k
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GSEA-class file (.cls) parsing error message
gsea
6.3 years ago snguyen268 • 0
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
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
0
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1
reply
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
Comment: deseq2 results by sajadahmad41454 • 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results by swbarnes2 ★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Dylan.Sheerin • 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie by Gordon Smyth 50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma by Gordon Smyth 50k
No, it does not mean that. `voom()` uses the design matrix, including the W covariates, to compute precision weights but not to adjust the …
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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