Showing : GSEA • reset
0
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13
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2.2k
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Gage and setp argument
gsea gage
8.0 years ago • updated 7.9 years ago peter.chernek • 0
1
vote
4
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2.3k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 7.5 years ago by ★ 1.2k • written 7.7 years ago by ▴ 110
9
votes
6
replies
5.5k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 7.9 years ago by 50k • written 7.9 years ago by ▴ 20
0
votes
5
replies
1.6k
views
gene set (enrichment) analysis
gsea gsa
updated 8.1 years ago by ★ 1.0k • written 8.1 years ago by ▴ 670
1
vote
2
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2.4k
views
GSVA for single sample
gsea gsva ssgsea
6.2 years ago jaison75 ▴ 20
3
votes
3
replies
1.6k
views
Enrichment Analysis with only GeneSymbols
R GSEA rna-seq scRna-Seq
updated 5.2 years ago by ★ 3.0k • written 5.2 years ago by ▴ 50
0
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3
replies
1.7k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 5.9 years ago by 41k • written 5.9 years ago by • 0
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 8.4 years ago by ★ 3.3k • written 8.4 years ago by ▴ 40
2
votes
4
replies
3.0k
views
Arguments for camera (gene set analysis)
camera GSEA
updated 8.2 years ago by ★ 13k • written 8.2 years ago by ▴ 10
8
votes
16
replies
5.6k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 9.4 years ago by ★ 1.1k • written 9.4 years ago by ▴ 10
2
votes
4
replies
1.6k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.1 years ago by 50k • written 8.1 years ago by ▴ 20
8
votes
5
replies
3.4k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.0 years ago by 50k • written 5.0 years ago by ▴ 110
7
votes
8
replies
11k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 12 months ago by ★ 4.0k • written 7.7 years ago by ▴ 20
1
vote
2
replies
2.1k
views
how to perform pre ranked GSEA in R?
r microarray statistics GSEA
updated 7.1 years ago by • 0 • written 9.2 years ago by ▴ 80
9
votes
13
replies
6.4k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 11 weeks ago by ★ 4.0k • written 2.1 years ago by ▴ 30
0
votes
1
reply
2.5k
views
ClusterProfiler can't load gmt file
GSEA clusterprofiler gmt
updated 7.7 years ago by ★ 1.2k • written 7.7 years ago by • 0
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea gsea
updated 7.3 years ago by ▴ 240 • written 7.3 years ago by ▴ 110
0
votes
6
replies
2.6k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage gsea rnaseq
updated 9.0 years ago by ★ 1.6k • written 9.0 years ago by • 0
5
votes
11
replies
1.8k
views
Appropriate methodologies for using various inputs(GOs, gene-sets) for mroast testing
limma mroast GSEA GO illumina human ht-12 v4
updated 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
1
vote
2
replies
904
views
giving weight to DEG from limma output
limma GSEA
updated 8.1 years ago by ★ 28k • written 8.1 years ago by ▴ 20
0
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4
replies
1.9k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways gsea egsea gage
updated 7.6 years ago by ▴ 40 • written 7.6 years ago by • 0
2
votes
3
replies
1.6k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
7.3 years ago • updated 7.2 years ago Pekka Kohonen ▴ 190
0
votes
7
replies
2.0k
views
Statistic for GSA
gsea concept gsa
updated 7.2 years ago by ▴ 190 • written 7.2 years ago by ▴ 730
0
votes
3
replies
2.3k
views
topGO - treating up- and down-regulated genes separately
topGO GSEA pathway analysis
updated 7.1 years ago by ▴ 730 • written 7.1 years ago by • 0
1
vote
1
reply
1.2k
views
Python Module from Kim and Volsky (2005) PAGE: Parametric Analysis of Gene Set Enrichment paper?
GSEA PAGE microarray differential gene expression pathway analysis
updated 7.1 years ago by ★ 3.9k • written 7.1 years ago by • 0
0
votes
1
reply
1.9k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 7.0 years ago by ★ 1.6k • written 7.0 years ago by • 0
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.2 years ago by 41k • written 5.2 years ago by • 0
0
votes
1
reply
806
views
Qusage/nlme package for adding random effects in gene set enrichment analysis
GSEA Qusage
5.1 years ago Diana ▴ 10
2
votes
4
replies
2.4k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.3 years ago by • 0 • written 5.1 years ago by ▴ 40
2
votes
2
replies
3.1k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 4.8 years ago by ▴ 70 • written 4.8 years ago by • 0
7
votes
11
replies
2.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.0 years ago by ★ 3.3k • written 4.0 years ago by ▴ 60
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.8 years ago by ★ 3.3k • written 3.8 years ago by ▴ 40
0
votes
1
reply
803
views
Need help with FoldGO input -> FuncAnnotGroupsTopGO function
FoldGO GSEA
3.4 years ago lessismore ▴ 20
2
votes
1
reply
972
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 years ago by • 0
0
votes
1
reply
573
views
choosing rank for GSEA
gsea DESeq2
updated 6 months ago by ★ 4.0k • written 6 months ago by • 0
7
votes
6
replies
2.1k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 16 months ago by 50k • written 16 months ago by ▴ 30
0
votes
3
replies
1.9k
views
Should 0 values for gene counts be removed prior to ssGSEA/GSVA analysis?
GSEA GSVA
updated 18 months ago by ▴ 60 • written 22 months ago by • 0
2
votes
4
replies
1.3k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 21 months ago by 50k • written 21 months ago by ▴ 10
0
votes
2
replies
334
views
The order of those tied genes will be arbitrary, which may produce unexpected results.
fgsea gsea
5 weeks ago • updated 25 days ago Gordon • 0
2
votes
3
replies
907
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 18 months ago by • 0 • written 18 months ago by • 0
0
votes
1
reply
1.0k
views
GSEA using custom GO annotations
RNASeq GSEA
updated 2.1 years ago by ★ 3.3k • written 2.1 years ago by ▴ 10
0
votes
2
replies
3.2k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA GeneSetEnrichment
22 months ago Bhavana • 0
4
votes
3
replies
216
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 5 weeks ago by • 0
0
votes
3
replies
1.3k
views
gseaplot2 from enrichplot for gene set enrichment analysis comparing two datasets
enrichplot GSEA clusterProfiler
updated 6 months ago by • 0 • written 8 months ago by • 0
2
votes
3
replies
916
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 15 months ago by ▴ 40 • written 15 months ago by • 0
1
vote
1
reply
963
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 9 months ago by 50k • written 9 months ago by • 0
1
vote
5
replies
2.0k
views
FGSEA only runs with <1000 permutations
fgsea gsea
updated 6.8 years ago by ▴ 240 • written 6.8 years ago by • 0
2
votes
1
reply
4.2k
views
Intepretation of Z scores for gene set enrichment analysis in MAST
MAST scRNA GSEA
updated 6.8 years ago by ▴ 270 • written 6.8 years ago by • 0
1
vote
1
reply
1.1k
views
two-color microarray - Gene Set Enrichment Analysis
Twocolor microarray GSEA
updated 6.7 years ago by 50k • written 6.7 years ago by • 0
0
votes
2
replies
1.6k
views
Resolved- GSEAbase: goSlim function, pb with counts
GSEA GO goSlim
6.6 years ago maeva.mollion • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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