Showing : GSEa • reset
1
vote
4
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329
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Error in gseDO function
DOSE gsea
5 weeks ago Javier • 0
0
votes
2
replies
484
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
3 months ago Gordon • 0
2
votes
1
reply
349
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 3 months ago by ★ 4.0k • written 3 months ago by ▴ 10
4
votes
3
replies
367
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 3 months ago by • 0
0
votes
1
reply
849
views
choosing rank for GSEA
gsea DESeq2
updated 8 months ago by ★ 4.2k • written 8 months ago by • 0
0
votes
3
replies
1.5k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 8 months ago by • 0 • written 11 months ago by • 0
0
votes
0
replies
691
views
using fgsea to compare two datasets
GSEA fgsea
11 months ago Cen • 0
1
vote
1
reply
1.1k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 12 months ago by 51k • written 12 months ago by • 0
7
votes
8
replies
12k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 14 months ago by ★ 4.2k • written 7.9 years ago by ▴ 20
2
votes
3
replies
1.1k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 18 months ago by ▴ 40 • written 18 months ago by • 0
0
votes
1
reply
639
views
GSA type of input data
GSEA GSA vst
updated 18 months ago by 42k • written 18 months ago by ▴ 50
0
votes
1
reply
922
views
DGE genes are not available in GSEA
dge gsea
updated 19 months ago by ★ 4.0k • written 19 months ago by • 0
7
votes
6
replies
2.4k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 18 months ago by 51k • written 19 months ago by ▴ 50
2
votes
3
replies
982
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 20 months ago by • 0 • written 20 months ago by • 0
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 23 months ago by 51k • written 23 months ago by ▴ 10
0
votes
3
replies
2.1k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 20 months ago by ▴ 60 • written 2.0 years ago by • 0
0
votes
2
replies
3.7k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.0 years ago Bhavana • 0
0
votes
1
reply
1.2k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.3 years ago by ★ 3.3k • written 2.3 years ago by ▴ 10
10
votes
13
replies
7.3k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 5 months ago by ★ 4.2k • written 2.3 years ago by ▴ 50
2
votes
1
reply
1.0k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.3 years ago by ★ 3.9k • written 3.3 years ago by • 0
0
votes
2
replies
2.6k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.4 years ago Emilia ▴ 30
0
votes
1
reply
859
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.6 years ago lessismore ▴ 20
2
votes
1
reply
2.2k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.0 years ago by ★ 3.3k • written 4.0 years ago by ▴ 50
7
votes
11
replies
2.6k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.2 years ago by ★ 3.3k • written 4.2 years ago by ▴ 60
2
votes
2
replies
3.4k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.0 years ago by ▴ 70 • written 5.0 years ago by • 0
8
votes
5
replies
3.7k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.2 years ago by 51k • written 5.2 years ago by ▴ 110
2
votes
4
replies
2.6k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.5 years ago by • 0 • written 5.3 years ago by ▴ 40
0
votes
1
reply
858
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.3 years ago Diana ▴ 10
0
votes
1
reply
2.7k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.3 years ago aboumarshal • 0
3
votes
7
replies
27k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.4 years ago by 42k • written 5.4 years ago by • 0
3
votes
3
replies
1.7k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.4 years ago by ★ 3.0k • written 5.4 years ago by ▴ 60
0
votes
3
replies
1.4k
views
gseaplot vertical line
clusterProfiler gsea
updated 5.5 years ago by 0 • written 5.6 years ago by • 0
0
votes
2
replies
1.4k
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 5.7 years ago by ▴ 50 • written 5.7 years ago by ▴ 10
0
votes
1
reply
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 5.7 years ago by 42k • written 5.7 years ago by • 0
0
votes
2
replies
1.7k
views
gene set enrichment analysis
GSEA GSA
updated 5.7 years ago by 51k • written 5.7 years ago by ▴ 670
0
votes
2
replies
1.3k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
5.8 years ago santos22903 • 0
5
votes
7
replies
2.8k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 5.9 years ago by 51k • written 5.9 years ago by ▴ 10
0
votes
0
replies
1.1k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
5.9 years ago l.brown ▴ 10
0
votes
3
replies
3.0k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
6.0 years ago atakanekiz ▴ 30
0
votes
3
replies
1.8k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.1 years ago by 42k • written 6.1 years ago by • 0
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.1 years ago martin.busch • 0
1
vote
1
reply
1.4k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.2 years ago by 51k • written 6.2 years ago by ▴ 20
2
votes
2
replies
4.2k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.3 years ago by ★ 1.2k • written 6.3 years ago by • 0
1
vote
2
replies
2.5k
views
GSVA for single sample
gsea gsva ssgsea
6.4 years ago jaison75 ▴ 20
0
votes
2
replies
1.8k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.4 years ago by ★ 1.2k • written 6.4 years ago by • 0
1
vote
1
reply
1.9k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.5 years ago Stane ▴ 40
0
votes
0
replies
1.3k
views
GSEA-class file (.cls) parsing error message
gsea
6.5 years ago snguyen268 • 0
0
votes
1
reply
2.4k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.6 years ago giuseppe0525 • 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.7 years ago • updated 6.6 years ago giuseppe0525 • 0
4
votes
1
reply
3.5k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.7 years ago by ▴ 270 • written 6.7 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Comment: limma comparison for small sample size and how to get covariance matrix by Gordon Smyth 51k
Your MDS plot is better than before, but you are still not following the recommendation for making for making such plots given in the limma…
Comment: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
Also, ``` > result <- mapUniProt( from = "EMBL-GenBank-DDBJ_CDS", to = "UniProtKB", query = c("ACF95883.1") ) > result From…
Comment: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
Ugh, here's the link https://www.uniprot.org/id-mapping/uniprotkb/dd08aa16774d98ef087dc3bd708582012bba49e2/overview?fields=accession%2Cre…
Answer: Mapping Between GenBank ID's and Uniprot by James W. MacDonald 66k
The input should be 'EMBL-GenBank-DDBJ_CDS", as that is a GenBank ID.
Answer: XCMS2 of orbitrap data by Elodie • 0
Hi, I have the same question, I have acquired MS2 data with PRM analysis and inclusion lists of several ions. I have a list of product ion…
Votes
Answer: EPIC array hg38 annotation?
Answer: Why does DESeq2 give negative log2 fold change in treatment vs control for some
Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: Ranking the GSEA Results
Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
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