Showing : Gsea • reset
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Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
gsea mice org.Mm.eg.db
updated 8 weeks ago by 67k • written 8 weeks ago by • 0
1
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2
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1.1k
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How to use compareCluster in ClusterProfiler?
RNASeqData GSEA clusterProfiler
written 3 months ago by • 0
0
votes
1
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503
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Should the expression data be filtered for `Protein-Coding Genes` before Running ssGSEA?
ssgsea GSVA gsea
updated 4 months ago by ★ 1.0k • written 4 months ago by • 0
1
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4
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785
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Error in gseDO function
DOSE gsea
7 months ago • updated 6 months ago Javier • 0
0
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2
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1.0k
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The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
9 months ago • updated 8 months ago Gordon • 0
2
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2
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788
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Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
written 9 months ago by ▴ 10
4
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3
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695
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Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 9 months ago by • 0
0
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1
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1.4k
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choosing rank for GSEA
gsea DESeq2
updated 14 months ago by ★ 4.6k • written 14 months ago by • 0
0
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3
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2.2k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 14 months ago by • 0 • written 16 months ago by • 0
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0
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919
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using fgsea to compare two datasets
GSEA fgsea
17 months ago Cen • 0
1
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1
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1.6k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 17 months ago by 52k • written 17 months ago by • 0
8
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8
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14k
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GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 20 months ago by ★ 4.6k • written 8.4 years ago by ▴ 20
2
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3
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1.4k
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 23 months ago by ▴ 40 • written 23 months ago by • 0
0
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1
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780
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GSA type of input data
GSEA GSA vst
updated 24 months ago by 43k • written 24 months ago by ▴ 70
0
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1
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1.2k
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DGE genes are not available in GSEA
dge gsea
updated 2.0 years ago by ★ 4.1k • written 2.0 years ago by • 0
7
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6
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3.1k
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Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 24 months ago by 52k • written 2.0 years ago by ▴ 70
2
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3
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1.3k
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
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4
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1.7k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.4 years ago by 52k • written 2.4 years ago by ▴ 10
0
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3
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2.8k
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Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 2.1 years ago by ▴ 60 • written 2.5 years ago by • 0
0
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2
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4.8k
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What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
2.5 years ago Bhavana • 0
0
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1
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1.7k
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GSEA using custom GO annotations
RNASeq GSEA
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by ▴ 10
12
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13
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9.6k
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GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 10 months ago by ★ 4.6k • written 2.8 years ago by ▴ 70
2
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1
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1.2k
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GSEA generate genesets
pathway KEGGREST GSEA
updated 3.8 years ago by ★ 4.0k • written 3.8 years ago by • 0
0
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2
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3.2k
views
gene set enrichment analysis with enrichKEGG (clusterProfiler) returns very few enriched pathways
clusterProfiler KEGG GSEA
3.9 years ago Emilia ▴ 40
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1
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1.0k
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
4.1 years ago lessismore ▴ 20
2
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1
reply
2.7k
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
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11
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3.1k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.7 years ago by ★ 3.4k • written 4.7 years ago by ▴ 60
2
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2
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4.1k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 5.5 years ago by ▴ 70 • written 5.5 years ago by • 0
8
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5
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4.3k
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How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.6 years ago by 52k • written 5.6 years ago by ▴ 120
2
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4
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3.0k
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Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 4.0 years ago by • 0 • written 5.8 years ago by ▴ 40
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1
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1.0k
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Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.8 years ago Diana ▴ 10
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1
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3.3k
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Useful of Normal Enrichment Score (NES) in GSEA
GSEA
5.8 years ago aboumarshal • 0
3
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7
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28k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.8 years ago by 43k • written 5.8 years ago by • 0
3
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3
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2.0k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.8 years ago by ★ 3.0k • written 5.8 years ago by ▴ 60
0
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3
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1.6k
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gseaplot vertical line
clusterProfiler gsea
updated 6.0 years ago by 0 • written 6.1 years ago by • 0
0
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2
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1.6k
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GSEA using TFs as the gene set
GSEA transcription factor binding site enrichment analysis
updated 6.1 years ago by ▴ 50 • written 6.1 years ago by ▴ 10
0
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1
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1.4k
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Using TPM of a specific isoform as a phenotype for gene set enrichment analysis
deseq2 gsea tpm rnaseq salmon rna seq
updated 6.2 years ago by 43k • written 6.2 years ago by • 0
0
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2
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1.9k
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gene set enrichment analysis
GSEA GSA
updated 6.2 years ago by 52k • written 6.2 years ago by ▴ 670
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2
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1.5k
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Warning in bayes fit in MAST GSEA
MAST GSEA bayesglm.fit
6.3 years ago santos22903 • 0
5
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7
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3.4k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 6.4 years ago by 52k • written 6.4 years ago by ▴ 10
0
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0
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1.2k
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Job: 2 Postdoc Positions in computational epigenetics and non-coding RNA analysis (#CNPD08)
bioinformatician job rna-seq chipseq gsea python Job
6.4 years ago l.brown ▴ 10
0
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3
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3.6k
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fgsea p-values are mostly the same upon analysis
fgsea gsea sc-rnaseq
6.4 years ago atakanekiz ▴ 30
0
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3
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2.0k
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Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.5 years ago by 43k • written 6.5 years ago by • 0
1
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2
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2.0k
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ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
6.5 years ago martin.busch • 0
1
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1
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1.6k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.7 years ago by 52k • written 6.7 years ago by ▴ 20
2
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2
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4.7k
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Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.8 years ago by ★ 1.2k • written 6.8 years ago by • 0
1
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2
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2.7k
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GSVA for single sample
gsea gsva ssgsea
6.9 years ago jaison75 ▴ 20
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2
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2.0k
views
merging gseaResult objects
clusterprofiler gsea
updated 6.9 years ago by ★ 1.2k • written 6.9 years ago by • 0
1
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1
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2.2k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
7.0 years ago Stane ▴ 40
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0
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1.5k
views
GSEA-class file (.cls) parsing error message
gsea
7.0 years ago snguyen268 • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
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Popular Question to martin.grigorov ▴ 10
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