Showing : GSEABase • reset
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News: Gene Set Enrichment Analysis in Bioconductor course
GSEABase GeneSetEnrichment goseq
8 months ago info ▴ 10
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1.9k
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Problems with GSEA
GSEABase
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
2
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2
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1.2k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
14 months ago Assa Yeroslaviz ★ 1.5k
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2
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639
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Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
18 months ago Yveto • 0
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928
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"Counts" in enrichGO
GSEABase
updated 21 months ago by ▴ 10 • written 21 months ago by • 0
1
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1
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2.5k
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Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 3.6 years ago by ★ 3.4k • written 3.6 years ago by • 0
3
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1
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1.5k
views
GSEABase::getBroadSets returns error with the latest MSigDB version
GSEABase
updated 4.9 years ago by 25k • written 4.9 years ago by ▴ 60
7
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11
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4.1k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 5.5 years ago by ★ 3.4k • written 5.5 years ago by ▴ 60
3
votes
4
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2.9k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
5.7 years ago • updated 2.7 years ago samwhite ▴ 20
7
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9
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5.3k
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GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
5.7 years ago • updated 2.6 years ago samwhite ▴ 20
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3
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2.2k
views
GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
6.3 years ago sandeep.amberkar18 ▴ 10
2
votes
2
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2.1k
views
GSEABase: how to extract shortDescription from GeneSetCollection object
GSEABase
updated 6.6 years ago by 25k • written 6.6 years ago by ★ 4.1k
1
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1
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2.6k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 7.4 years ago by ▴ 170
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3
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2.4k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 7.4 years ago by 43k • written 7.4 years ago by • 0
3
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3
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2.2k
views
convert Gene collection to gene list for camera function
limma GSEABase
updated 7.7 years ago by 68k • written 7.7 years ago by • 0
2
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2
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1.9k
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 7.9 years ago by ★ 3.4k • written 7.9 years ago by ▴ 60
1
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2
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2.8k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
8.2 years ago maeva.mollion • 0
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1.4k
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Does GSEABase support organismDb objects?
GSEABase
8.3 years ago sandmann.t ▴ 70
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2
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2.4k
views
Problem with GeneSetCollection after updating R devel packages.
bug gseabase example
8.8 years ago jcrodriguez ▴ 20
2
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2
replies
1.8k
views
Using GeneSetCollection objects of GSEABase in piano package
piano gseabase
8.8 years ago Lluís Revilla Sancho ▴ 760
2
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3
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1.8k
views
Probable bug in GSEABase package.
software error bug gseabase
8.8 years ago jcrodriguez ▴ 20
1
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2
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2.2k
views
Question on GeneSetCollection in GSEABase
gseabase geneset
updated 8.8 years ago by 25k • written 8.8 years ago by • 0
1
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1
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2.2k
views
GSEABase getGmt() fails when more than 1 line contains duplicates
gseabase bug
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 10
9
votes
6
replies
7.1k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 9.4 years ago by 53k • written 9.4 years ago by ▴ 20
0
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3
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5.0k
views
Creating custom geneset
gseabase
9.8 years ago • updated 9.7 years ago pbachali ▴ 50
8
votes
16
replies
7.5k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 11.0 years ago by ★ 1.1k • written 11.0 years ago by ▴ 10
0
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3
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2.3k
views
Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 11.6 years ago by ★ 13k • written 11.6 years ago by ▴ 70
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5
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4.1k
views
Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 11.6 years ago by ★ 1.3k • written 11.6 years ago by ▴ 680
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1.4k
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correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
12.9 years ago Robert Castelo ★ 3.4k
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1.5k
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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
13.8 years ago Valerie Obenchain ★ 6.8k
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4
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2.7k
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conversion of geneset species ID
GSEABase GSEABase
updated 14.2 years ago by 25k • written 14.2 years ago by ▴ 930
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1
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1.6k
views
creating a UniprotIdentifier within GSEABase
Annotation Cancer hgu95av2 convert GSEABase Annotation Cancer hgu95av2 convert GSEABase
updated 14.3 years ago by 25k • written 14.3 years ago by ▴ 910
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0
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2.2k
views
GO with R and Bioconductor
Transcription Annotation GO GOstats biomaRt topGO GSEABase goseq Transcription Annotation
14.7 years ago Duke ▴ 210
0
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1
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2.1k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 15.0 years ago by 25k • written 15.0 years ago by ▴ 20
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0
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1.5k
views
creating GO and KEGG gene set collections for E. coli
GO GSEABase gage GO GSEABase gage
15.0 years ago Clémentine Dressaire ▴ 120
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1.6k
views
GSEABase and Broad Inst Sets
Annotation hgu133plus2 hgu95av2 GSEABase Annotation hgu133plus2 hgu95av2 GSEABase
updated 15.4 years ago by 25k • written 15.4 years ago by ▴ 930
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3
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2.1k
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Romer and symbols2indices query
probe limma GSEABase probe limma GSEABase
15.5 years ago Gordon Smyth 53k
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3
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1.9k
views
GSEAbase and limma
limma GSEABase limma GSEABase
updated 16.0 years ago by 53k • written 16.0 years ago by ▴ 840
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3
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2.0k
views
GeneSetCollection using EntrezID
Annotation Pathways GSEABase Annotation Pathways GSEABase
updated 16.0 years ago by 25k • written 16.0 years ago by ▴ 840
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3
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1.8k
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question using GSEABase
GO GOstats topGO GSEABase GO GOstats topGO GSEABase
updated 16.5 years ago by 25k • written 16.5 years ago by ▴ 80
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1
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1.7k
views
GSEABase GOCollection wrong ontology
Annotation GO hgu133plus2 affy GSEABase Annotation GO hgu133plus2 affy GSEABase
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 330
0
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0
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1.7k
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GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
16.8 years ago Paul Geeleher ★ 1.3k
2
votes
2
replies
1.8k
views
GSEA
GSEABase GSEABase
updated 17.0 years ago by 25k • written 17.0 years ago by ★ 1.0k
0
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1
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1.8k
views
GSEABase
GO illuminaHumanv2 lumi GSEABase GO illuminaHumanv2 lumi GSEABase
updated 17.0 years ago by 25k • written 17.0 years ago by ▴ 280
0
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2
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1.6k
views
using GSEAlm with GO geneSetCollections
GO affy goTools Category GSEABase GSEAlm GO affy goTools Category GSEABase GSEAlm
updated 17.0 years ago by ▴ 90 • written 17.0 years ago by ▴ 830
0
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0
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1.5k
views
GSEA packages that depend on GSEABase?
GO GSEABase GO GSEABase
17.3 years ago Mark W Kimpel ▴ 830
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3
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2.9k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
17.3 years ago anna freni sterrantino ▴ 120
0
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0
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1.5k
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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
17.3 years ago Chanchal Kumar ▴ 130
0
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3
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2.2k
views
GeneSetCollection from GSEA
Proteomics GSEABase Proteomics GSEABase
updated 17.7 years ago by 25k • written 17.7 years ago by ▴ 70
0
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5
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2.9k
views
GSEA and Broad gene sets
Pathways GSEABase Pathways GSEABase
updated 18.0 years ago by ★ 1.2k • written 18.0 years ago by ▴ 30
50 results • Page 1 of 1
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Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Comment: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif by Matthew Thornton ▴ 380
WOW! Thank you so much for the information. I will do this.
Comment: "Watched Tags" are being erased rather than updated by RalphSavage99 • 0
Thanks for sharing https://github.com/Bioconductor/support.bioconductor.org/issues/112
Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
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Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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