Showing : gseabase • reset
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
11 days ago Frances Turner ▴ 20
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1
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874
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News: Gene Set Enrichment Analysis in Bioconductor course
GSEABase GeneSetEnrichment goseq
11 months ago • updated 10 months ago info ▴ 10
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1
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Problems with GSEA
GSEABase
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
2
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2
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1.3k
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fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
16 months ago Assa Yeroslaviz ★ 1.5k
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717
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Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
20 months ago Yveto • 0
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1.0k
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"Counts" in enrichGO
GSEABase
updated 23 months ago by ▴ 10 • written 23 months ago by • 0
1
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1
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2.7k
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Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 3.8 years ago by ★ 3.4k • written 3.8 years ago by • 0
3
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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
7
votes
11
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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
3
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4
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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
7
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9
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5.6k
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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
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3
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2.3k
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GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
6.5 years ago sandeep.amberkar18 ▴ 10
2
votes
2
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2.2k
views
GSEABase: how to extract shortDescription from GeneSetCollection object
GSEABase
updated 6.8 years ago by 25k • written 6.8 years ago by ★ 4.1k
1
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1
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2.7k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 7.6 years ago by ▴ 170
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3
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2.5k
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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
3
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3
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2.5k
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
2
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2
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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
1
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2
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2.9k
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RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
8.4 years ago maeva.mollion • 0
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1.4k
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Does GSEABase support organismDb objects?
GSEABase
8.5 years ago sandmann.t ▴ 70
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2
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2.4k
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Problem with GeneSetCollection after updating R devel packages.
bug gseabase example
9.0 years ago jcrodriguez ▴ 20
2
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2
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1.8k
views
Using GeneSetCollection objects of GSEABase in piano package
piano gseabase
9.0 years ago Lluís Revilla Sancho ▴ 760
2
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3
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1.9k
views
Probable bug in GSEABase package.
software error bug gseabase
9.0 years ago jcrodriguez ▴ 20
1
vote
2
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2.3k
views
Question on GeneSetCollection in GSEABase
gseabase geneset
updated 9.0 years ago by 25k • written 9.0 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
9
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6
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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
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3
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5.2k
views
Creating custom geneset
gseabase
9.9 years ago pbachali ▴ 50
8
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16
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7.8k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 11.2 years ago by ★ 1.1k • written 11.2 years ago by ▴ 10
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3
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2.4k
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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
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5
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4.3k
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
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1.5k
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correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
13.1 years ago Robert Castelo ★ 3.4k
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1.6k
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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
14.0 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 14.4 years ago by 25k • written 14.4 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 14.5 years ago by 25k • written 14.5 years ago by ▴ 910
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2.2k
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GO with R and Bioconductor
Transcription Annotation GO GOstats biomaRt topGO GSEABase goseq Transcription Annotation
14.9 years ago Duke ▴ 210
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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 15.2 years ago by 25k • written 15.2 years ago by ▴ 20
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creating GO and KEGG gene set collections for E. coli
GO GSEABase gage GO GSEABase gage
15.2 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 15.6 years ago by 25k • written 15.6 years ago by ▴ 930
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3
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2.2k
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Romer and symbols2indices query
probe limma GSEABase probe limma GSEABase
15.7 years ago Gordon Smyth 53k
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3
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2.0k
views
GSEAbase and limma
limma GSEABase limma GSEABase
updated 16.2 years ago by 53k • written 16.2 years ago by ▴ 840
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3
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2.0k
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GeneSetCollection using EntrezID
Annotation Pathways GSEABase Annotation Pathways GSEABase
updated 16.2 years ago by 25k • written 16.2 years ago by ▴ 840
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1.9k
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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
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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 16.9 years ago by 25k • written 16.9 years ago by ▴ 330
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1.7k
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GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
17.0 years ago Paul Geeleher ★ 1.3k
2
votes
2
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1.9k
views
GSEA
GSEABase GSEABase
updated 17.2 years ago by 25k • written 17.2 years ago by ★ 1.0k
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1
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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
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2
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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
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0
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1.5k
views
GSEA packages that depend on GSEABase?
GO GSEABase GO GSEABase
17.5 years ago Mark W Kimpel ▴ 830
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3
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3.0k
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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
17.5 years ago anna freni sterrantino ▴ 120
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1.6k
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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
17.5 years ago Chanchal Kumar ▴ 130
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3
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2.3k
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GeneSetCollection from GSEA
Proteomics GSEABase Proteomics GSEABase
updated 17.9 years ago by 25k • written 17.9 years ago by ▴ 70
51 results • Page 1 of 2
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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k
The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k
Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…
Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0
Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…
Votes
A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen
Comment: limpa analysis advice
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
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