Showing : GSEA • reset
13
votes
2
replies
4.6k
views
Best method/package for Gene Set Enrichment Analysis in microarrays?
GSEA goseq topgo gega gostats
updated 8.5 years ago by ★ 3.3k • written 8.5 years ago by ▴ 40
9
votes
6
replies
5.6k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 7.9 years ago by 50k • written 8.0 years ago by ▴ 20
9
votes
13
replies
6.8k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.2k • written 2.2 years ago by ▴ 40
8
votes
16
replies
5.7k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 9.5 years ago by ★ 1.1k • written 9.5 years ago by ▴ 10
8
votes
5
replies
3.6k
views
How to get t-statistic values using edgeR?
r edger t-statistic fgsea gsea
updated 5.1 years ago by 50k • written 5.1 years ago by ▴ 110
7
votes
8
replies
12k
views
GSEA preranked analysis downstream of DEseq2
deseq2 gsea rnaseq
updated 13 months ago by ★ 4.2k • written 7.8 years ago by ▴ 20
7
votes
6
replies
2.2k
views
Implementation of the "original" GSEA algorithm in R
clusterProfiler GSEA fgsea
updated 17 months ago by 50k • written 17 months ago by ▴ 40
7
votes
11
replies
2.5k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.1 years ago by ★ 3.3k • written 4.1 years ago by ▴ 60
5
votes
7
replies
2.6k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 5.8 years ago by 50k • written 5.8 years ago by ▴ 10
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 9.0 years ago by ★ 28k • written 9.0 years ago by ▴ 830
4
votes
3
replies
275
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 9 weeks ago by • 0
4
votes
1
reply
3.3k
views
GSEA using clusterprofileR
clusterprofiler gsea
updated 6.6 years ago by ▴ 260 • written 6.6 years ago by ▴ 30
3
votes
7
replies
26k
views
DESeq2 log2FC shrink before GSEA or not?
deseq2 gsea rnaseq gene espression
updated 5.2 years ago by 42k • written 5.2 years ago by • 0
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 ▴ 60
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
2
votes
4
replies
1.7k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
updated 17 days ago by ▴ 10 • written 7.4 years ago by ▴ 190
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea gsea
updated 7.4 years ago by ▴ 260 • written 7.4 years ago by ▴ 110
2
votes
4
replies
2.5k
views
Are singscore scores comparable between gene sets?
singscore GSVA GSEA subtypes geneset
updated 3.4 years ago by • 0 • written 5.2 years ago by ▴ 40
2
votes
2
replies
3.2k
views
ClusterProfiler GSEA with geneList
clusterProfiler GSEA geneList
updated 4.9 years ago by ▴ 70 • written 4.9 years ago by • 0
2
votes
1
reply
2.1k
views
pre-filtering gene sets for GSVA/ssGSEA
gsea ssgsea gsva pathways
updated 3.9 years ago by ★ 3.3k • written 3.9 years ago by ▴ 50
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
6.8 years ago cabezasdelafuented ▴ 10
2
votes
1
reply
991
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.2 years ago by ★ 3.9k • written 3.2 years ago by • 0
2
votes
1
reply
4.3k
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
2
votes
4
replies
1.4k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 22 months ago by 50k • written 22 months ago by ▴ 10
2
votes
4
replies
1.7k
views
A rational way for selecting the number of DEG with significant p-value for GSEA
GSEA DEG
updated 8.2 years ago by 50k • written 8.2 years ago by ▴ 20
2
votes
1
reply
248
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 8 weeks ago by ★ 4.0k • written 9 weeks ago by ▴ 10
2
votes
3
replies
931
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 18 months ago by • 0 • written 19 months ago by • 0
2
votes
6
replies
12k
views
GSEA using clusterProfiler
GSEA clusterProfiler
6.5 years ago giuseppe0525 • 0
2
votes
3
replies
969
views
GSEA for paired methylation data
missMethyl GSEA minfi methylGSA
updated 16 months ago by ▴ 40 • written 16 months ago by • 0
2
votes
2
replies
4.1k
views
Clusterprofiler - MSigDB gene set analysis - Updated
clusterprofiler GSEA MSIGDB
updated 6.2 years ago by ★ 1.2k • written 6.2 years ago by • 0
1
vote
5
replies
2.1k
views
FGSEA only runs with <1000 permutations
fgsea gsea
updated 6.8 years ago by ▴ 260 • written 6.8 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 7.2 years ago by ★ 4.0k • written 7.2 years ago by • 0
1
vote
0
replies
1.4k
views
enrichment analysis for gene pairs
go gostats category gsea
8.6 years ago Hector Corrada Bravo ▴ 60
1
vote
1
reply
1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.4 years ago Stane ▴ 40
1
vote
2
replies
2.1k
views
how to perform pre ranked GSEA in R?
r microarray statistics GSEA
updated 7.2 years ago by • 0 • written 9.2 years ago by ▴ 80
1
vote
1
reply
1.0k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 10 months ago by 50k • written 10 months ago by • 0
1
vote
0
replies
1.3k
views
Gene Set Testing or GSEA for functional annotation of co-expressed ncRNA and coding genes
gsea ncrna coexpression gene set analysis gene set testing
8.1 years ago m.fletcher ▴ 20
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea gsva ssgsea
6.3 years ago jaison75 ▴ 20
1
vote
4
replies
2.3k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 7.5 years ago by ★ 1.2k • written 7.8 years ago by ▴ 110
1
vote
2
replies
911
views
giving weight to DEG from limma output
limma GSEA
updated 8.2 years ago by ★ 28k • written 8.2 years ago by ▴ 20
1
vote
1
reply
1.4k
views
Where is it possible to find gene sets in rdata format for GSEA ?
Gsea rattus norvegicus
updated 6.1 years ago by 50k • written 6.1 years ago by ▴ 20
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
1
vote
2
replies
1.8k
views
ReactomePA / Reactome: GSEA error message
reactomepa reactome gsea fgsea
5.9 years ago martin.busch • 0
0
votes
1
reply
612
views
GSA type of input data
GSEA GSA vst
updated 17 months ago by 42k • written 17 months ago by ▴ 40
0
votes
1
reply
2.4k
views
gseaplot() function of clusterProfiler went wrong
gsea clusterprofiler
6.5 years ago giuseppe0525 • 0
0
votes
6
replies
2.7k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage gsea rnaseq
updated 9.1 years ago by ★ 1.6k • written 9.1 years ago by • 0
0
votes
0
replies
1.1k
views
GSEA with variant proportions as input
GSEA Variant Proportions Input
8.8 years ago manali.rupji • 0
0
votes
5
replies
1.7k
views
gene set (enrichment) analysis
gsea gsa
updated 8.2 years ago by ★ 1.0k • written 8.2 years ago by ▴ 670
0
votes
13
replies
2.2k
views
Gage and setp argument
gsea gage
8.0 years ago peter.chernek • 0
0
votes
1
reply
2.5k
views
ClusterProfiler can't load gmt file
GSEA clusterprofiler gmt
updated 7.8 years ago by ★ 1.2k • written 7.8 years ago by • 0
50 results • Page 1 of 1
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Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function by Robert Castelo ★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Votes
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DESeq2: add annotations (from data frame) to DESeqDataSet
Add new columns to DESeqResults from text file by matching rownames.
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