Showing : Gsea • reset
0
votes
4
replies
602
views
How to sort negative log2FC or FC in RNAseq for GSEA?
DESeq2 GSEA clusterProfiler
11 weeks ago Quang NN ▴ 10
1
vote
8
replies
1.2k
views
Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 5 months ago by 68k • written 5 months ago by • 0
1
vote
2
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2.2k
views
How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 7 months ago by • 0
0
votes
1
reply
762
views
Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 8 months ago by ★ 1.1k • written 8 months ago by • 0
1
vote
4
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1.1k
views
Error in gseDO function
DOSE gsea
10 months ago Javier • 0
0
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2
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1.5k
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
12 months ago Gordon • 0
2
votes
2
replies
1.1k
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 12 months ago by ▴ 10
4
votes
3
replies
915
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 12 months ago by • 0
0
votes
1
reply
1.9k
views
choosing rank for GSEA
gsea DESeq2
updated 17 months ago by ★ 4.8k • written 18 months ago by • 0
0
votes
3
replies
2.7k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 17 months ago by • 0 • written 20 months ago by • 0
0
votes
0
replies
1.1k
views
using fgsea to compare two datasets
GSEA fgsea
21 months ago Cen • 0
1
vote
1
reply
1.9k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 21 months ago by 52k • written 21 months ago by • 0
8
votes
8
replies
15k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 23 months ago by ★ 4.8k • written 8.7 years ago by ▴ 20
2
votes
3
replies
1.7k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 2.3 years ago by ▴ 40 • written 2.3 years ago by • 0
0
votes
1
reply
868
views
GSA type of input data
GSEA GSA vst
updated 2.3 years ago by 43k • written 2.3 years ago by ▴ 70
0
votes
1
reply
1.4k
views
DGE genes are not available in GSEA
dge gsea
updated 2.3 years ago by ★ 4.1k • written 2.3 years ago by • 0
7
votes
6
replies
4.0k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 2.3 years ago by 52k • written 2.3 years ago by ▴ 70
2
votes
3
replies
1.4k
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 2.4 years ago by • 0 • written 2.4 years ago by • 0
2
votes
4
replies
1.8k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.7 years ago by 52k • written 2.7 years ago by ▴ 10
0
votes
3
replies
3.3k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.4 years ago by ▴ 60 • written 2.8 years ago by • 0
0
votes
2
replies
5.5k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.8 years ago Bhavana • 0
0
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1
reply
2.0k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 3.1 years ago by ★ 3.4k • written 3.1 years ago by ▴ 10
12
votes
13
replies
11k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 14 months ago by ★ 4.8k • written 3.1 years ago by ▴ 70
2
votes
1
reply
1.2k
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 4.1 years ago by ★ 4.0k • written 4.1 years ago by • 0
0
votes
2
replies
3.8k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
4.2 years ago Emilia ▴ 40
0
votes
1
reply
1.1k
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
4.4 years ago lessismore ▴ 20
2
votes
1
reply
3.0k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 50
7
votes
11
replies
3.5k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.9 years ago by ★ 3.4k • written 4.9 years ago by ▴ 60
2
votes
2
replies
4.5k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.8 years ago by ▴ 70 • written 5.8 years ago by • 0
8
votes
5
replies
4.6k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.9 years ago by 52k • written 5.9 years ago by ▴ 120
2
votes
4
replies
3.3k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 4.3 years ago by • 0 • written 6.1 years ago by ▴ 40
0
votes
1
reply
1.1k
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
6.1 years ago Diana ▴ 10
0
votes
1
reply
3.7k
views
Useful of Normal Enrichment Score (NES) in GSEA
GSEA
6.1 years ago aboumarshal • 0
3
votes
7
replies
29k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 6.1 years ago by 43k • written 6.1 years ago by • 0
3
votes
3
replies
2.4k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 6.1 years ago by ★ 3.0k • written 6.1 years ago by ▴ 60
0
votes
3
replies
1.6k
views
gseaplot vertical line
clusterProfiler gsea
updated 6.3 years ago by 0 • written 6.4 years ago by • 0
0
votes
2
replies
1.9k
views
GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 6.4 years ago by ▴ 50 • written 6.4 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
0
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2
replies
2.1k
views
gene set enrichment analysis
GSEA GSA
updated 6.5 years ago by 52k • written 6.5 years ago by ▴ 670
0
votes
2
replies
1.6k
views
Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.6 years ago santos22903 • 0
5
votes
7
replies
3.8k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 10
0
votes
0
replies
1.3k
views
Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
6.7 years ago l.brown ▴ 10
0
votes
3
replies
3.9k
views
fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
6.7 years ago atakanekiz ▴ 30
0
votes
3
replies
2.2k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.8 years ago by 43k • written 6.8 years ago by • 0
1
vote
2
replies
2.2k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.8 years ago martin.busch • 0
1
vote
1
reply
1.7k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 7.0 years ago by 52k • written 7.0 years ago by ▴ 20
2
votes
2
replies
5.0k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 7.1 years ago by ★ 1.2k • written 7.1 years ago by • 0
1
vote
2
replies
2.9k
views
GSVA for single sample
gsea gsva ssgsea
7.2 years ago jaison75 ▴ 20
0
votes
2
replies
2.2k
views
merging gseaResult objects
clusterprofiler gsea
updated 7.2 years ago by ★ 1.2k • written 7.2 years ago by • 0
1
vote
1
reply
2.4k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
7.3 years ago Stane ▴ 40
50 results • Page 1 of 1
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Answer: how to use `arrayWeightsQuick()`? by Gordon Smyth 52k
Yes, that is the correct way to use `arrayWeightsQuick`. Thanks for pointing out that there is still a reference to `arrayWeightsSimple` i…
Answer: fast apply on RleList by story.benjamin ▴ 20
solved with viewApply (code is simplified below) + map reduce on chrs test.split <- split(test.gr,seqnames(test.gr)) final.st…
Comment: fast apply on RleList by story.benjamin ▴ 20
Hi James, thanks for the reply. I ultimately figured it out ... viewApply showed a massive speed increase for me (see other answer) - I was…
Answer: fast apply on RleList by James W. MacDonald 68k
There is already a 'mean' function that will dispatch on an `RleList` that you can use. I don't have a long `RleList` in hand to test it on…
Answer: Custom CDF creation for HTA 2.0 array using GTF annotation by James W. MacDonald 68k
It doesn't appear that Manhong Dai is working at UM any longer, and the webpage appears to have fallen into disrepair (for example, the lin…
Votes
annotation EpicV2
Answer: fast apply on RleList
Answer: BiocParallel_1.40.1.tar.gz not available
Modelling gene program dynamics across time with {lemur}
A: DESeq2 one group vs multiple groups comparison in presence of batch effect
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