Showing : GSEABase • reset
9
votes
6
replies
7.4k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 9.6 years ago by 53k • written 9.6 years ago by ▴ 20
8
votes
16
replies
7.7k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 11.1 years ago by ★ 1.1k • written 11.1 years ago by ▴ 10
7
votes
11
replies
4.4k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 5.7 years ago by ★ 3.4k • written 5.7 years ago by ▴ 60
7
votes
9
replies
5.6k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
5.9 years ago • updated 2.8 years ago samwhite ▴ 20
3
votes
4
replies
3.1k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
5.9 years ago • updated 2.9 years ago samwhite ▴ 20
3
votes
3
replies
2.4k
views
convert Gene collection to gene list for camera function
limma GSEABase
updated 7.9 years ago by 68k • written 7.9 years ago by • 0
3
votes
1
reply
1.6k
views
GSEABase::getBroadSets returns error with the latest MSigDB version
GSEABase
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 60
2
votes
2
replies
1.9k
views
GSEA
GSEABase GSEABase
updated 17.2 years ago by 25k • written 17.2 years ago by ★ 1.0k
2
votes
2
replies
2.0k
views
Error thrown by GSEABase::getBroadSets function: Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'archived'
GSEABase getBroadSets invalid BroadCollection category archived MSigDB v6.1
updated 8.1 years ago by ★ 3.4k • written 8.1 years ago by ▴ 60
2
votes
2
replies
2.2k
views
GSEABase: how to extract shortDescription from GeneSetCollection object
GSEABase
updated 6.7 years ago by 25k • written 6.7 years ago by ★ 4.1k
2
votes
2
replies
1.3k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
16 months ago Assa Yeroslaviz ★ 1.5k
2
votes
3
replies
1.8k
views
Probable bug in GSEABase package.
software error bug gseabase
9.0 years ago jcrodriguez ▴ 20
2
votes
2
replies
1.8k
views
Using GeneSetCollection objects of GSEABase in piano package
piano gseabase
9.0 years ago Lluís Revilla Sancho ▴ 760
1
vote
1
reply
2.6k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 3.8 years ago by ★ 3.4k • written 3.8 years ago by • 0
1
vote
1
reply
2.3k
views
GSEABase getGmt() fails when more than 1 line contains duplicates
gseabase bug
updated 9.3 years ago by 25k • written 9.3 years ago by ▴ 10
1
vote
2
replies
2.9k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
8.4 years ago maeva.mollion • 0
1
vote
1
reply
2.7k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 7.6 years ago by ▴ 170
1
vote
2
replies
2.3k
views
Question on GeneSetCollection in GSEABase
gseabase geneset
updated 9.0 years ago by 25k • written 9.0 years ago by • 0
0
votes
4
replies
2.7k
views
conversion of geneset species ID
GSEABase GSEABase
updated 14.4 years ago by 25k • written 14.4 years ago by ▴ 930
0
votes
0
replies
1.5k
views
[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
14.0 years ago Valerie Obenchain ★ 6.8k
0
votes
0
replies
1.5k
views
correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
13.1 years ago Robert Castelo ★ 3.4k
0
votes
5
replies
4.2k
views
Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 11.8 years ago by ★ 1.3k • written 11.8 years ago by ▴ 680
0
votes
3
replies
2.4k
views
Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 11.8 years ago by ★ 13k • written 11.8 years ago by ▴ 70
0
votes
3
replies
5.1k
views
Creating custom geneset
gseabase
9.9 years ago pbachali ▴ 50
0
votes
0
replies
1.6k
views
creating GO and KEGG gene set collections for E. coli
GO GSEABase gage GO GSEABase gage
15.2 years ago Clémentine Dressaire ▴ 120
0
votes
0
replies
1.4k
views
Does GSEABase support organismDb objects?
GSEABase
8.5 years ago sandmann.t ▴ 70
0
votes
3
replies
2.5k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
0
votes
3
replies
2.3k
views
GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
6.5 years ago sandeep.amberkar18 ▴ 10
0
votes
1
reply
863
views
News: Gene Set Enrichment Analysis in Bioconductor course
GSEABase GeneSetEnrichment goseq
11 months ago • updated 10 months ago info ▴ 10
0
votes
1
reply
2.2k
views
Problems with GSEA
GSEABase
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
votes
1
reply
1.0k
views
"Counts" in enrichGO
GSEABase
updated 23 months ago by ▴ 10 • written 23 months ago by • 0
0
votes
0
replies
37
views
News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
4 days ago Frances Turner ▴ 20
0
votes
2
replies
709
views
Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
20 months ago Yveto • 0
0
votes
2
replies
2.4k
views
Problem with GeneSetCollection after updating R devel packages.
bug gseabase example
8.9 years ago jcrodriguez ▴ 20
0
votes
1
reply
2.1k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 15.1 years ago by 25k • written 15.1 years ago by ▴ 20
0
votes
5
replies
3.0k
views
GSEA and Broad gene sets
Pathways GSEABase Pathways GSEABase
updated 18.1 years ago by ★ 1.2k • written 18.1 years ago by ▴ 30
0
votes
3
replies
2.3k
views
GeneSetCollection from GSEA
Proteomics GSEABase Proteomics GSEABase
updated 17.9 years ago by 25k • written 17.9 years ago by ▴ 70
0
votes
0
replies
1.6k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
17.5 years ago Chanchal Kumar ▴ 130
0
votes
3
replies
3.0k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
17.5 years ago anna freni sterrantino ▴ 120
0
votes
0
replies
1.5k
views
GSEA packages that depend on GSEABase?
GO GSEABase GO GSEABase
17.5 years ago Mark W Kimpel ▴ 830
0
votes
2
replies
1.7k
views
using GSEAlm with GO geneSetCollections
GO affy goTools Category GSEABase GSEAlm GO affy goTools Category GSEABase GSEAlm
updated 17.2 years ago by ▴ 90 • written 17.2 years ago by ▴ 830
0
votes
1
reply
1.9k
views
GSEABase
GO illuminaHumanv2 lumi GSEABase GO illuminaHumanv2 lumi GSEABase
updated 17.2 years ago by 25k • written 17.2 years ago by ▴ 280
0
votes
0
replies
1.7k
views
GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
17.0 years ago Paul Geeleher ★ 1.3k
0
votes
1
reply
1.7k
views
GSEABase GOCollection wrong ontology
Annotation GO hgu133plus2 affy GSEABase Annotation GO hgu133plus2 affy GSEABase
updated 16.9 years ago by 25k • written 16.9 years ago by ▴ 330
0
votes
3
replies
1.9k
views
question using GSEABase
GO GOstats topGO GSEABase GO GOstats topGO GSEABase
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 80
0
votes
3
replies
2.0k
views
GeneSetCollection using EntrezID
Annotation Pathways GSEABase Annotation Pathways GSEABase
updated 16.2 years ago by 25k • written 16.2 years ago by ▴ 840
0
votes
3
replies
2.0k
views
GSEAbase and limma
limma GSEABase limma GSEABase
updated 16.2 years ago by 53k • written 16.2 years ago by ▴ 840
0
votes
3
replies
2.2k
views
Romer and symbols2indices query
probe limma GSEABase probe limma GSEABase
15.7 years ago Gordon Smyth 53k
0
votes
1
reply
1.6k
views
GSEABase and Broad Inst Sets
Annotation hgu133plus2 hgu95av2 GSEABase Annotation hgu133plus2 hgu95av2 GSEABase
updated 15.5 years ago by 25k • written 15.5 years ago by ▴ 930
0
votes
0
replies
2.2k
views
GO with R and Bioconductor
Transcription Annotation GO GOstats biomaRt topGO GSEABase goseq Transcription Annotation
14.9 years ago Duke ▴ 210
51 results • Page 1 of 2
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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