Showing : gsea • reset
0
votes
4
replies
376
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
9 days ago • updated 7 days ago Quang NN ▴ 10
1
vote
8
replies
1.1k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 3 months ago by 67k • written 3 months ago by • 0
1
vote
2
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1.4k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 4 months ago by • 0
0
votes
1
reply
583
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 5 months ago by ★ 1.0k • written 5 months ago by • 0
1
vote
4
replies
867
views
Error in gseDO function
DOSE gsea
8 months ago Javier • 0
0
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2
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1.2k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
10 months ago Gordon • 0
2
votes
2
replies
874
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 10 months ago by ▴ 10
4
votes
3
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769
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 10 months ago by • 0
0
votes
1
reply
1.5k
views
choosing rank for GSEA
gsea DESeq2
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
0
votes
3
replies
2.4k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 15 months ago by • 0 • written 17 months ago by • 0
0
votes
0
replies
950
views
using fgsea to compare two datasets
GSEA fgsea
18 months ago Cen • 0
1
vote
1
reply
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
votes
8
replies
14k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 21 months ago by ★ 4.6k • written 8.5 years ago by ▴ 20
2
votes
3
replies
1.5k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
0
votes
1
reply
808
views
GSA type of input data
GSEA GSA vst
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 70
0
votes
1
reply
1.3k
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
votes
6
replies
3.4k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 2.1 years ago by 52k • written 2.1 years ago by ▴ 70
2
votes
3
replies
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
votes
4
replies
1.7k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.5 years ago by 52k • written 2.5 years ago by ▴ 10
0
votes
3
replies
2.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.2 years ago by ▴ 60 • written 2.6 years ago by • 0
0
votes
2
replies
5.0k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.6 years ago Bhavana • 0
0
votes
1
reply
1.8k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.9 years ago by ★ 3.4k • written 2.9 years ago by ▴ 10
12
votes
13
replies
10k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 months ago by ★ 4.6k • written 2.9 years ago by ▴ 70
2
votes
1
reply
1.2k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.9 years ago by ★ 4.0k • written 3.9 years ago by • 0
0
votes
2
replies
3.4k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
4.0 years ago Emilia ▴ 40
0
votes
1
reply
1.0k
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
4.2 years ago lessismore ▴ 20
2
votes
1
reply
2.8k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.5 years ago by ★ 3.4k • written 4.6 years ago by ▴ 50
7
votes
11
replies
3.2k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.8 years ago by ★ 3.4k • written 4.8 years ago by ▴ 60
2
votes
2
replies
4.2k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.6 years ago by ▴ 70 • written 5.6 years ago by • 0
8
votes
5
replies
4.4k
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
votes
4
replies
3.1k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 4.1 years ago by • 0 • written 5.9 years ago by ▴ 40
0
votes
1
reply
1.0k
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.9 years ago Diana ▴ 10
0
votes
1
reply
3.4k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.9 years ago aboumarshal • 0
3
votes
7
replies
29k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.9 years ago by 43k • written 5.9 years ago by • 0
3
votes
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
votes
3
replies
1.6k
views
gseaplot vertical line
clusterProfiler gsea
updated 6.1 years ago by 0 • written 6.2 years ago by • 0
0
votes
2
replies
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
votes
1
reply
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 6.3 years ago by 43k • written 6.3 years ago by • 0
0
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2
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2.0k
views
gene set enrichment analysis
GSEA GSA
updated 6.3 years ago by 52k • written 6.3 years ago by ▴ 670
0
votes
2
replies
1.5k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.4 years ago santos22903 • 0
5
votes
7
replies
3.6k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 6.5 years ago by 52k • written 6.5 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
6.5 years ago l.brown ▴ 10
0
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3
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3.7k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
6.5 years ago atakanekiz ▴ 30
0
votes
3
replies
2.1k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.6 years ago by 43k • written 6.6 years ago by • 0
1
vote
2
replies
2.1k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.6 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 6.8 years ago by 52k • written 6.8 years ago by ▴ 20
2
votes
2
replies
4.8k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
1
vote
2
replies
2.8k
views
GSVA for single sample
gsea gsva ssgsea
7.0 years ago jaison75 ▴ 20
0
votes
2
replies
2.1k
views
merging gseaResult objects
clusterprofiler gsea
updated 7.0 years ago by ★ 1.2k • written 7.0 years ago by • 0
1
vote
1
reply
2.3k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
7.1 years ago Stane ▴ 40
50 results • Page 1 of 1
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Comment: Identifying potentially associated gene set to drug response using GSVA by kl2023gege • 0
Thanks for sharing. You gotta check out Sprunki Phase Games on [Sprunki Phase](https://sprunkiphase.net). It's a wild ride of tunes and tw…
Answer: I am having issues with bowtie2_build by James W. MacDonald 67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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