Showing : GSEABase • reset
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News: Online RNA-seq analysis course 26-29th Janury
EnhancedVolcano GSEABase pheatmap Workshop DESeq2
14 days ago Frances Turner ▴ 20
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News: Gene Set Enrichment Analysis in Bioconductor course
GSEABase GeneSetEnrichment goseq
11 months ago info ▴ 10
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Problems with GSEA
GSEABase
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
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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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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
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GSEABase::getBroadSets returns error with the latest MSigDB version
GSEABase
updated 5.1 years ago by 25k • written 5.1 years ago by ▴ 60
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4.5k
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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
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4
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GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
5.9 years ago • updated 2.9 years ago samwhite ▴ 20
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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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2.4k
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GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
6.5 years ago sandeep.amberkar18 ▴ 10
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GSEABase: how to extract shortDescription from GeneSetCollection object
GSEABase
updated 6.8 years ago by 25k • written 6.8 years ago by ★ 4.1k
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2.7k
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Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 7.6 years ago by ▴ 170
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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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2.5k
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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
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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
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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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Does GSEABase support organismDb objects?
GSEABase
8.6 years ago sandmann.t ▴ 70
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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
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2
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1.8k
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Using GeneSetCollection objects of GSEABase in piano package
piano gseabase
9.0 years ago Lluís Revilla Sancho ▴ 760
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3
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1.9k
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Probable bug in GSEABase package.
software error bug gseabase
9.0 years ago jcrodriguez ▴ 20
1
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2
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2.3k
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Question on GeneSetCollection in GSEABase
gseabase geneset
updated 9.0 years ago by 25k • written 9.0 years ago by • 0
1
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1
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2.3k
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GSEABase getGmt() fails when more than 1 line contains duplicates
gseabase bug
updated 9.4 years ago by 25k • written 9.4 years ago by ▴ 10
9
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6
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7.4k
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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
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Creating custom geneset
gseabase
10.0 years ago • updated 9.9 years ago pbachali ▴ 50
8
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16
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7.8k
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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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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
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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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correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
13.1 years ago Robert Castelo ★ 3.4k
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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
14.0 years ago Valerie Obenchain ★ 6.8k
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2.8k
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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
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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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2.2k
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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
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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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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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2.0k
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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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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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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
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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
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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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1.9k
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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1.7k
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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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1.5k
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GSEA packages that depend on GSEABase?
GO GSEABase GO GSEABase
17.5 years ago Mark W Kimpel ▴ 830
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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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Answer: Array weights in dpcDE by Gordon Smyth 53k
The uncertainty of quantification is fully accounted for in the dpcDE() analysis, including in the computation of sample weights. Your use…
Answer: lfc shrinkage estimator in DESeq2 by Michael Love 43k
Try the vignette which has a lot of information on these type of questions.
Comment: limpa analysis advice by Gordon Smyth 53k
The DPC slope is beta1. The estimated slopes for your data look pretty low, lower than I've ever used for a real dataset. Nevertheless, as …
Comment: limpa analysis advice by SamGG ▴ 360
Thanks for your feedback and for reassuring me. :-) As you suggested, I tried dpcCN() and set the slope to 0.7 in addition to the standard…
Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0
Good point, I hadn't considered the fact quantitative `time` implies a (logit-)linear response *to* time. You're correct that I haven't exp…
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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