Showing : GSEABase • reset
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Problems with GSEA
GSEABase
updated 7 days ago by ★ 4.1k • written 7 days ago by • 0
2
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2
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767
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fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
4 months ago Assa Yeroslaviz ★ 1.5k
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2
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414
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Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
8 months ago Yveto • 0
0
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1
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627
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"Counts" in enrichGO
GSEABase
updated 11 months ago by ▴ 10 • written 11 months ago by • 0
1
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1
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1.9k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.8 years ago by ★ 3.4k • written 2.8 years ago by • 0
3
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1
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1.3k
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GSEABase::getBroadSets returns error with the latest MSigDB version
GSEABase
updated 4.1 years ago by 25k • written 4.1 years ago by ▴ 60
7
votes
11
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3.2k
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
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4
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2.3k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
4.9 years ago • updated 23 months ago samwhite ▴ 20
7
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9
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4.3k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
4.9 years ago • updated 22 months ago samwhite ▴ 20
0
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3
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1.9k
views
GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
5.5 years ago sandeep.amberkar18 ▴ 10
2
votes
2
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1.8k
views
GSEABase: how to extract shortDescription from GeneSetCollection object
GSEABase
updated 5.8 years ago by 25k • written 5.8 years ago by ★ 4.1k
1
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1
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2.2k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 6.6 years ago by ▴ 170
0
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3
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2.1k
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Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.6 years ago by 43k • written 6.6 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 6.9 years ago by 67k • written 6.9 years ago by • 0
2
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2
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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 7.1 years ago by ★ 3.4k • written 7.1 years ago by ▴ 60
1
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2
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2.5k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
7.4 years ago maeva.mollion • 0
0
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0
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1.2k
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Does GSEABase support organismDb objects?
GSEABase
7.6 years ago sandmann.t ▴ 70
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2
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2.1k
views
Problem with GeneSetCollection after updating R devel packages.
bug gseabase example
8.0 years ago jcrodriguez ▴ 20
2
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2
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1.5k
views
Using GeneSetCollection objects of GSEABase in piano package
piano gseabase
8.0 years ago Lluís Revilla Sancho ▴ 760
2
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3
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1.5k
views
Probable bug in GSEABase package.
software error bug gseabase
8.0 years ago jcrodriguez ▴ 20
1
vote
2
replies
1.8k
views
Question on GeneSetCollection in GSEABase
gseabase geneset
updated 8.0 years ago by 25k • written 8.0 years ago by • 0
1
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1
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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
6.4k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 8.6 years ago by 52k • written 8.6 years ago by ▴ 20
0
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3
replies
4.4k
views
Creating custom geneset
gseabase
9.0 years ago pbachali ▴ 50
8
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16
replies
6.4k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 10.2 years ago by ★ 1.1k • written 10.2 years ago by ▴ 10
0
votes
3
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2.0k
views
Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 10.8 years ago by ★ 13k • written 10.8 years ago by ▴ 70
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5
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3.7k
views
Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 10.8 years ago by ★ 1.3k • written 10.8 years ago by ▴ 660
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0
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1.3k
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correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
12.1 years ago Robert Castelo ★ 3.4k
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0
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1.4k
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[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
13.0 years ago Valerie Obenchain ★ 6.8k
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4
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2.4k
views
conversion of geneset species ID
GSEABase GSEABase
updated 13.4 years ago by 25k • written 13.4 years ago by ▴ 930
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1
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1.5k
views
creating a UniprotIdentifier within GSEABase
Annotation Cancer hgu95av2 convert GSEABase Annotation Cancer hgu95av2 convert GSEABase
updated 13.5 years ago by 25k • written 13.5 years ago by ▴ 910
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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
13.9 years ago Duke ▴ 210
0
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1
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1.9k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 14.2 years ago by 25k • written 14.2 years ago by ▴ 20
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0
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1.3k
views
creating GO and KEGG gene set collections for E. coli
GO GSEABase gage GO GSEABase gage
14.2 years ago Clémentine Dressaire ▴ 120
0
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1
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1.4k
views
GSEABase and Broad Inst Sets
Annotation hgu133plus2 hgu95av2 GSEABase Annotation hgu133plus2 hgu95av2 GSEABase
updated 14.6 years ago by 25k • written 14.6 years ago by ▴ 930
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3
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1.9k
views
Romer and symbols2indices query
probe limma GSEABase probe limma GSEABase
14.7 years ago Gordon Smyth 52k
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3
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1.7k
views
GSEAbase and limma
limma GSEABase limma GSEABase
updated 15.2 years ago by 52k • written 15.2 years ago by ▴ 840
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3
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1.7k
views
GeneSetCollection using EntrezID
Annotation Pathways GSEABase Annotation Pathways GSEABase
updated 15.2 years ago by 25k • written 15.2 years ago by ▴ 840
0
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3
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1.6k
views
question using GSEABase
GO GOstats topGO GSEABase GO GOstats topGO GSEABase
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 80
0
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1
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1.5k
views
GSEABase GOCollection wrong ontology
Annotation GO hgu133plus2 affy GSEABase Annotation GO hgu133plus2 affy GSEABase
updated 15.9 years ago by 25k • written 15.9 years ago by ▴ 330
0
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0
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1.5k
views
GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
16.0 years ago Paul Geeleher ★ 1.3k
2
votes
2
replies
1.6k
views
GSEA
GSEABase GSEABase
updated 16.2 years ago by 25k • written 16.2 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 16.2 years ago by 25k • written 16.2 years ago by ▴ 280
0
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2
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1.4k
views
using GSEAlm with GO geneSetCollections
GO affy goTools Category GSEABase GSEAlm GO affy goTools Category GSEABase GSEAlm
updated 16.2 years ago by ▴ 90 • written 16.2 years ago by ▴ 830
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0
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1.3k
views
GSEA packages that depend on GSEABase?
GO GSEABase GO GSEABase
16.5 years ago Mark W Kimpel ▴ 830
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3
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2.6k
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How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
16.5 years ago anna freni sterrantino ▴ 120
0
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0
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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
16.5 years ago Chanchal Kumar ▴ 130
0
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3
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2.0k
views
GeneSetCollection from GSEA
Proteomics GSEABase Proteomics GSEABase
updated 16.9 years ago by 25k • written 16.9 years ago by ▴ 70
0
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5
replies
2.5k
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
49 results • Page 1 of 1
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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