Showing : Gsea • reset
1
vote
8
replies
969
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 29 days ago by 67k • written 4 weeks ago by • 0
1
vote
2
replies
881
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 11 weeks ago by • 0
0
votes
1
reply
442
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 3 months ago by ★ 1.0k • written 3 months ago by • 0
1
vote
4
replies
709
views
Error in gseDO function
DOSE gsea
5 months ago Javier • 0
0
votes
2
replies
925
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
8 months ago • updated 7 months ago Gordon • 0
2
votes
2
replies
733
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 8 months ago by ▴ 10
4
votes
3
replies
642
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 8 months ago by • 0
0
votes
1
reply
1.3k
views
choosing rank for GSEA
gsea DESeq2
updated 13 months ago by ★ 4.5k • written 13 months ago by • 0
0
votes
3
replies
2.1k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 13 months ago by • 0 • written 15 months ago by • 0
0
votes
0
replies
885
views
using fgsea to compare two datasets
GSEA fgsea
16 months ago Cen • 0
1
vote
1
reply
1.5k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 16 months ago by 51k • written 16 months ago by • 0
8
votes
8
replies
13k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 19 months ago by ★ 4.5k • written 8.3 years ago by ▴ 20
2
votes
3
replies
1.4k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 22 months ago by ▴ 40 • written 22 months ago by • 0
0
votes
1
reply
760
views
GSA type of input data
GSEA GSA vst
updated 23 months ago by 42k • written 23 months ago by ▴ 70
0
votes
1
reply
1.2k
views
DGE genes are not available in GSEA
dge gsea
updated 23 months ago by ★ 4.1k • written 23 months ago by • 0
7
votes
6
replies
3.0k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 23 months ago by 51k • written 23 months ago by ▴ 70
2
votes
3
replies
1.2k
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 2.1 years ago by • 0 • written 2.1 years ago by • 0
2
votes
4
replies
1.6k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.3 years ago by 51k • written 2.3 years ago by ▴ 10
0
votes
3
replies
2.7k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.1 years ago by ▴ 60 • written 2.4 years ago by • 0
0
votes
2
replies
4.7k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.4 years ago Bhavana • 0
0
votes
1
reply
1.7k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.7 years ago by ★ 3.4k • written 2.7 years ago by ▴ 10
12
votes
13
replies
9.2k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 9 months ago by ★ 4.5k • written 2.7 years ago by ▴ 70
2
votes
1
reply
1.2k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.7 years ago by ★ 4.0k • written 3.7 years ago by • 0
0
votes
2
replies
3.1k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.8 years ago Emilia ▴ 40
0
votes
1
reply
986
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
4.0 years ago lessismore ▴ 20
2
votes
1
reply
2.6k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.4 years ago by ★ 3.4k • written 4.4 years ago by ▴ 50
7
votes
11
replies
3.0k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by ▴ 60
2
votes
2
replies
4.0k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.4 years ago by ▴ 70 • written 5.4 years ago by • 0
8
votes
5
replies
4.2k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.5 years ago by 51k • written 5.5 years ago by ▴ 120
2
votes
4
replies
2.9k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.9 years ago by • 0 • written 5.7 years ago by ▴ 40
0
votes
1
reply
985
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.7 years ago Diana ▴ 10
0
votes
1
reply
3.2k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.7 years ago aboumarshal • 0
3
votes
7
replies
28k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.7 years ago by 42k • written 5.7 years ago by • 0
3
votes
3
replies
2.0k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.7 years ago by ★ 3.0k • written 5.7 years ago by ▴ 60
0
votes
3
replies
1.5k
views
gseaplot vertical line
clusterProfiler gsea
updated 5.9 years ago by 0 • written 6.0 years ago by • 0
0
votes
2
replies
1.6k
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 6.0 years ago by ▴ 50 • written 6.0 years ago by ▴ 10
0
votes
1
reply
1.3k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 6.1 years ago by 42k • written 6.1 years ago by • 0
0
votes
2
replies
1.9k
views
gene set enrichment analysis
GSEA GSA
updated 6.1 years ago by 51k • written 6.1 years ago by ▴ 670
0
votes
2
replies
1.4k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.2 years ago santos22903 • 0
5
votes
7
replies
3.3k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 6.3 years ago by 51k • written 6.3 years ago by ▴ 10
0
votes
0
replies
1.2k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
6.3 years ago l.brown ▴ 10
0
votes
3
replies
3.5k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
6.3 years ago atakanekiz ▴ 30
0
votes
3
replies
2.0k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
1
vote
2
replies
2.0k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.4 years ago martin.busch • 0
1
vote
1
reply
1.6k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.6 years ago by 51k • written 6.6 years ago by ▴ 20
2
votes
2
replies
4.7k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.7 years ago by ★ 1.2k • written 6.7 years ago by • 0
1
vote
2
replies
2.7k
views
GSVA for single sample
gsea gsva ssgsea
6.8 years ago jaison75 ▴ 20
0
votes
2
replies
2.0k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
1
vote
1
reply
2.2k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.9 years ago Stane ▴ 40
0
votes
0
replies
1.5k
views
GSEA-class file (.cls) parsing error message
gsea
6.9 years ago snguyen268 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0
The updated version worked well on my data. Thank you!
Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Votes
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
A: correcting the batch effects in Limma and SVA
Awards • All
Scholar to Haibo Liu ▴ 20
Popular Question to Talip ▴ 10
Popular Question to alexandre.blais ▴ 50
Popular Question to Fred Hutch (Recruiting) ▴ 40
Scholar to Gordon Smyth 51k
Locations • All
United States, 5 minutes ago
Türkiye, 9 minutes ago
WEHI, Melbourne, Australia, 1 hour ago
Türkiye, 1 hour ago
EMBL Heidelberg, 1 hour ago
Traffic: 778 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6