Showing : gseabase • reset
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117
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News: Gene Set Enrichment Analysis in Bioconductor course
GSEABase GeneSetEnrichment goseq
10 days ago • updated 1 day ago info ▴ 10
0
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1
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387
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Problems with GSEA
GSEABase
updated 5 weeks ago by ★ 4.1k • written 5 weeks ago by • 0
2
votes
2
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822
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fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
5 months ago Assa Yeroslaviz ★ 1.5k
0
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2
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441
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Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
9 months ago Yveto • 0
0
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1
reply
694
views
"Counts" in enrichGO
GSEABase
updated 12 months ago by ▴ 10 • written 12 months ago by • 0
1
vote
1
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2.0k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.9 years ago by ★ 3.4k • written 2.9 years ago by • 0
3
votes
1
reply
1.3k
views
GSEABase::getBroadSets returns error with the latest MSigDB version
GSEABase
updated 4.2 years ago by 25k • written 4.2 years ago by ▴ 60
7
votes
11
replies
3.3k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.8 years ago by ★ 3.4k • written 4.8 years ago by ▴ 60
3
votes
4
replies
2.4k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
5.0 years ago • updated 24 months ago samwhite ▴ 20
7
votes
9
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4.4k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
5.0 years ago • updated 23 months ago samwhite ▴ 20
0
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3
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2.0k
views
GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
5.6 years ago sandeep.amberkar18 ▴ 10
2
votes
2
replies
1.9k
views
GSEABase: how to extract shortDescription from GeneSetCollection object
GSEABase
updated 5.9 years ago by 25k • written 5.9 years ago by ★ 4.1k
1
vote
1
reply
2.3k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 6.7 years ago by ▴ 170
0
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3
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2.1k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.7 years ago by 43k • written 6.7 years ago by • 0
3
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3
replies
1.9k
views
convert Gene collection to gene list for camera function
limma GSEABase
updated 7.0 years ago by 68k • written 7.0 years ago by • 0
2
votes
2
replies
1.7k
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 7.2 years ago by ★ 3.4k • written 7.2 years ago by ▴ 60
1
vote
2
replies
2.5k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
7.5 years ago maeva.mollion • 0
0
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0
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1.3k
views
Does GSEABase support organismDb objects?
GSEABase
7.6 years ago sandmann.t ▴ 70
0
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2
replies
2.1k
views
Problem with GeneSetCollection after updating R devel packages.
bug gseabase example
8.1 years ago jcrodriguez ▴ 20
2
votes
2
replies
1.5k
views
Using GeneSetCollection objects of GSEABase in piano package
piano gseabase
8.1 years ago Lluís Revilla Sancho ▴ 760
2
votes
3
replies
1.6k
views
Probable bug in GSEABase package.
software error bug gseabase
8.1 years ago jcrodriguez ▴ 20
1
vote
2
replies
1.8k
views
Question on GeneSetCollection in GSEABase
gseabase geneset
updated 8.1 years ago by 25k • written 8.1 years ago by • 0
1
vote
1
reply
2.0k
views
GSEABase getGmt() fails when more than 1 line contains duplicates
gseabase bug
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 10
9
votes
6
replies
6.5k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 8.7 years ago by 52k • written 8.7 years ago by ▴ 20
0
votes
3
replies
4.5k
views
Creating custom geneset
gseabase
9.0 years ago pbachali ▴ 50
8
votes
16
replies
6.6k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 10.3 years ago by ★ 1.1k • written 10.3 years ago by ▴ 10
0
votes
3
replies
2.1k
views
Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 10.9 years ago by ★ 13k • written 10.9 years ago by ▴ 70
0
votes
5
replies
3.7k
views
Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 10.9 years ago by ★ 1.3k • written 10.9 years ago by ▴ 680
0
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0
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1.3k
views
correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
12.2 years ago Robert Castelo ★ 3.4k
0
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0
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1.4k
views
[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
13.1 years ago Valerie Obenchain ★ 6.8k
0
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4
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2.4k
views
conversion of geneset species ID
GSEABase GSEABase
updated 13.5 years ago by 25k • written 13.5 years ago by ▴ 930
0
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1
reply
1.5k
views
creating a UniprotIdentifier within GSEABase
Annotation Cancer hgu95av2 convert GSEABase Annotation Cancer hgu95av2 convert GSEABase
updated 13.6 years ago by 25k • written 13.6 years ago by ▴ 910
0
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0
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2.0k
views
GO with R and Bioconductor
Transcription Annotation GO GOstats biomaRt topGO GSEABase goseq Transcription Annotation
14.0 years ago Duke ▴ 210
0
votes
1
reply
1.9k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 20
0
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0
replies
1.4k
views
creating GO and KEGG gene set collections for E. coli
GO GSEABase gage GO GSEABase gage
14.3 years ago Clémentine Dressaire ▴ 120
0
votes
1
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1.4k
views
GSEABase and Broad Inst Sets
Annotation hgu133plus2 hgu95av2 GSEABase Annotation hgu133plus2 hgu95av2 GSEABase
updated 14.7 years ago by 25k • written 14.7 years ago by ▴ 930
0
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3
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2.0k
views
Romer and symbols2indices query
probe limma GSEABase probe limma GSEABase
14.8 years ago Gordon Smyth 52k
0
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3
replies
1.7k
views
GSEAbase and limma
limma GSEABase limma GSEABase
updated 15.3 years ago by 52k • written 15.3 years ago by ▴ 840
0
votes
3
replies
1.8k
views
GeneSetCollection using EntrezID
Annotation Pathways GSEABase Annotation Pathways GSEABase
updated 15.3 years ago by 25k • written 15.3 years ago by ▴ 840
0
votes
3
replies
1.6k
views
question using GSEABase
GO GOstats topGO GSEABase GO GOstats topGO GSEABase
updated 15.8 years ago by 25k • written 15.8 years ago by ▴ 80
0
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1
reply
1.5k
views
GSEABase GOCollection wrong ontology
Annotation GO hgu133plus2 affy GSEABase Annotation GO hgu133plus2 affy GSEABase
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 330
0
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0
replies
1.5k
views
GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
16.1 years ago Paul Geeleher ★ 1.3k
2
votes
2
replies
1.7k
views
GSEA
GSEABase GSEABase
updated 16.3 years ago by 25k • written 16.3 years ago by ★ 1.0k
0
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1
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1.6k
views
GSEABase
GO illuminaHumanv2 lumi GSEABase GO illuminaHumanv2 lumi GSEABase
updated 16.3 years ago by 25k • written 16.3 years ago by ▴ 280
0
votes
2
replies
1.4k
views
using GSEAlm with GO geneSetCollections
GO affy goTools Category GSEABase GSEAlm GO affy goTools Category GSEABase GSEAlm
updated 16.3 years ago by ▴ 90 • written 16.3 years ago by ▴ 830
0
votes
0
replies
1.3k
views
GSEA packages that depend on GSEABase?
GO GSEABase GO GSEABase
16.6 years ago Mark W Kimpel ▴ 830
0
votes
3
replies
2.7k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
16.6 years ago anna freni sterrantino ▴ 120
0
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0
replies
1.4k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
16.6 years ago Chanchal Kumar ▴ 130
0
votes
3
replies
2.0k
views
GeneSetCollection from GSEA
Proteomics GSEABase Proteomics GSEABase
updated 17.0 years ago by 25k • written 17.0 years ago by ▴ 70
0
votes
5
replies
2.6k
views
GSEA and Broad gene sets
Pathways GSEABase Pathways GSEABase
updated 17.2 years ago by ★ 1.2k • written 17.2 years ago by ▴ 30
50 results • Page 1 of 1
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Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Answer: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
I strongly recommend to not concern yourself with these sorts of marginal problems because you're entering a realm in which you're entirely…
Comment: Problem using locateVariants() from the VariantAnnotation package by Marco • 0
Ok, I think I found the problem. By looking at the `locateVariants()` source code, I was able to pinpoint that the problems is when trying …
Comment: Conumee for EPIC and EPICv2 copy number by Adam • 0
As described on the [github](https://github.com/hovestadtlab/conumee2) the way to do this is using array_type = c("EPIC", "EPICv2") This i…
Comment: graper 1.22 Build is Broken by shepherl 4.1k
This is not an appropriate place to report this. this is for usage questions. maintainers are notified automatically when it is failing on …
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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