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
5.5k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 7.9 years ago by 50k • written 7.9 years ago by ▴ 20
9
votes
13
replies
6.6k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA GeneSetEnrichment DifferentialExpression
updated 3 months ago by ★ 4.1k • written 2.1 years ago by ▴ 30
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
8
votes
5
replies
3.5k
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 ★ 4.1k • written 7.8 years ago by ▴ 20
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 17 months ago by ▴ 30
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
5
votes
7
replies
2.6k
views
GSEA for RNA-seq analysis
GSEA Limma preranked GSEA tTest
updated 5.7 years ago by 50k • written 5.7 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 8.9 years ago by ★ 28k • written 8.9 years ago by ▴ 830
4
votes
3
replies
235
views
Problem converting msigdb Human symbols to Zebrafish in gmt format
msigdb gmt GSEA
written 7 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 41k • 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 ▴ 50
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
3
replies
1.6k
views
EGSEA usage with microarray data (with vooma)?
EGSEA gene set testing vooma limma voom gsea
7.3 years ago Pekka Kohonen ▴ 190
2
votes
1
reply
1.5k
views
Direction aware fgsea test
fgsea gsea
updated 7.3 years ago by ▴ 260 • written 7.3 years ago by ▴ 110
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 5.2 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
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
2
votes
3
replies
1.8k
views
custom annotation for GO enrichment
annotationforge GSEA clusterprofiler GO annotation
6.7 years ago cabezasdelafuented ▴ 10
2
votes
1
reply
979
views
GSEA generate genesets
pathway KEGGREST GSEA
updated 3.1 years ago by ★ 3.9k • written 3.1 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
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
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 8.2 years ago by ▴ 20
2
votes
1
reply
213
views
Only positive enrichment score in GSEA
clusterProfiler annotation gseGO gsea OrgDb
updated 6 weeks ago by ★ 3.9k • written 6 weeks ago by ▴ 10
2
votes
3
replies
916
views
system.file() failed to load .gmt file.
pathwayPCA Gsea
updated 18 months ago by • 0 • written 18 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
943
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 6.1 years ago by ★ 1.2k • written 6.1 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 7.1 years ago by ★ 3.9k • written 7.1 years ago by • 0
1
vote
0
replies
1.3k
views
enrichment analysis for gene pairs
go gostats category gsea
8.5 years ago Hector Corrada Bravo ▴ 60
1
vote
1
reply
1.8k
views
Inconsistency of results GSEA clusterprofiler
gsea clusterprofiler
6.3 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
986
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 9 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
8.0 years ago m.fletcher ▴ 20
1
vote
2
replies
2.4k
views
GSVA for single sample
gsea gsva ssgsea
6.2 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 7.7 years ago by ▴ 110
1
vote
2
replies
907
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 6.0 years ago by 50k • written 6.0 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
601
views
GSA type of input data
GSEA GSA vst
updated 16 months ago by 41k • written 16 months ago by ▴ 30
0
votes
1
reply
2.3k
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 9.0 years ago by ★ 1.6k • written 9.0 years ago by • 0
0
votes
0
replies
1.1k
views
GSEA with variant proportions as input
GSEA Variant Proportions Input
8.7 years ago manali.rupji • 0
0
votes
5
replies
1.7k
views
gene set (enrichment) analysis
gsea gsa
updated 8.1 years ago by ★ 1.0k • written 8.1 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 7.7 years ago by ★ 1.2k • written 7.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
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