Showing : gseabase • reset
2
votes
2
replies
654
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
10 weeks ago Assa Yeroslaviz ★ 1.5k
0
votes
2
replies
351
views
Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
6 months ago Yveto • 0
0
votes
1
reply
524
views
"Counts" in enrichGO
GSEABase
updated 9 months ago by ▴ 10 • written 9 months ago by • 0
1
vote
1
reply
1.7k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.6 years ago by ★ 3.4k • written 2.6 years ago by • 0
3
votes
1
reply
1.2k
views
GSEABase::getBroadSets returns error with the latest MSigDB version
GSEABase
updated 3.9 years ago by 25k • written 3.9 years ago by ▴ 60
7
votes
11
replies
3.0k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase annotation gsea gsva GeneSetCollection
updated 4.6 years ago by ★ 3.4k • written 4.6 years ago by ▴ 60
3
votes
4
replies
2.1k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
4.8 years ago • updated 20 months ago samwhite ▴ 20
7
votes
9
replies
4.0k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
4.8 years ago • updated 20 months ago samwhite ▴ 20
0
votes
3
replies
1.9k
views
GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
5.3 years ago sandeep.amberkar18 ▴ 10
2
votes
2
replies
1.8k
views
GSEABase: how to extract shortDescription from GeneSetCollection object
GSEABase
updated 5.6 years ago by 25k • written 5.6 years ago by ★ 4.1k
1
vote
1
reply
2.2k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 6.4 years ago by ▴ 170
0
votes
3
replies
2.0k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA DESeq2 gseabase GSEA
updated 6.4 years ago by 42k • written 6.4 years ago by • 0
3
votes
3
replies
1.8k
views
convert Gene collection to gene list for camera function
limma GSEABase
updated 6.7 years ago by 67k • written 6.7 years ago by • 0
2
votes
2
replies
1.6k
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 6.9 years ago by ★ 3.4k • written 6.9 years ago by ▴ 60
1
vote
2
replies
2.4k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
7.2 years ago maeva.mollion • 0
0
votes
0
replies
1.2k
views
Does GSEABase support organismDb objects?
GSEABase
7.4 years ago sandmann.t ▴ 70
0
votes
2
replies
2.0k
views
Problem with GeneSetCollection after updating R devel packages.
bug gseabase example
7.8 years ago jcrodriguez ▴ 20
2
votes
2
replies
1.4k
views
Using GeneSetCollection objects of GSEABase in piano package
piano gseabase
7.8 years ago Lluís Revilla Sancho ▴ 760
2
votes
3
replies
1.4k
views
Probable bug in GSEABase package.
software error bug gseabase
7.8 years ago jcrodriguez ▴ 20
1
vote
2
replies
1.7k
views
Question on GeneSetCollection in GSEABase
gseabase geneset
updated 7.8 years ago by 25k • written 7.8 years ago by • 0
1
vote
1
reply
1.9k
views
GSEABase getGmt() fails when more than 1 line contains duplicates
gseabase bug
updated 8.2 years ago by 25k • written 8.2 years ago by ▴ 10
9
votes
6
replies
6.2k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 8.4 years ago by 51k • written 8.4 years ago by ▴ 20
0
votes
3
replies
4.3k
views
Creating custom geneset
gseabase
8.8 years ago pbachali ▴ 50
8
votes
16
replies
6.2k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 10.0 years ago by ★ 1.1k • written 10.0 years ago by ▴ 10
0
votes
3
replies
2.0k
views
Running the GSEA algorithm
Microarray GeneSetEnrichment PGSEA GSEABase GSRI SeqGSEA Microarray GeneSetEnrichment GSRI
updated 10.6 years ago by ★ 13k • written 10.6 years ago by ▴ 70
0
votes
5
replies
3.6k
views
Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 10.6 years ago by ★ 1.3k • written 10.6 years ago by ▴ 660
0
votes
0
replies
1.2k
views
correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
11.9 years ago Robert Castelo ★ 3.4k
0
votes
0
replies
1.3k
views
[Rocky] - R code for PGSEA package to identify differentially expressed genes
GO affy limma GLAD PGSEA GSEABase GO affy limma GLAD PGSEA GSEABase
12.8 years ago Valerie Obenchain ★ 6.8k
0
votes
4
replies
2.3k
views
conversion of geneset species ID
GSEABase GSEABase
updated 13.2 years ago by 25k • written 13.2 years ago by ▴ 930
0
votes
1
reply
1.4k
views
creating a UniprotIdentifier within GSEABase
Annotation Cancer hgu95av2 convert GSEABase Annotation Cancer hgu95av2 convert GSEABase
updated 13.3 years ago by 25k • written 13.3 years ago by ▴ 910
0
votes
0
replies
1.9k
views
GO with R and Bioconductor
Transcription Annotation GO GOstats biomaRt topGO GSEABase goseq Transcription Annotation
13.7 years ago Duke ▴ 210
0
votes
1
reply
1.8k
views
Help with GSEA package
hu6800 cdf genefilter multtest affy gcrma siggenes annaffy GSEABase hu6800 cdf multtest
updated 14.0 years ago by 25k • written 14.0 years ago by ▴ 20
0
votes
0
replies
1.3k
views
creating GO and KEGG gene set collections for E. coli
GO GSEABase gage GO GSEABase gage
14.0 years ago Clémentine Dressaire ▴ 120
0
votes
1
reply
1.4k
views
GSEABase and Broad Inst Sets
Annotation hgu133plus2 hgu95av2 GSEABase Annotation hgu133plus2 hgu95av2 GSEABase
updated 14.4 years ago by 25k • written 14.4 years ago by ▴ 930
0
votes
3
replies
1.9k
views
Romer and symbols2indices query
probe limma GSEABase probe limma GSEABase
14.6 years ago • updated 14.5 years ago Gordon Smyth 51k
0
votes
3
replies
1.6k
views
GSEAbase and limma
limma GSEABase limma GSEABase
updated 15.0 years ago by 51k • written 15.0 years ago by ▴ 840
0
votes
3
replies
1.7k
views
GeneSetCollection using EntrezID
Annotation Pathways GSEABase Annotation Pathways GSEABase
updated 15.0 years ago by 25k • written 15.0 years ago by ▴ 840
0
votes
3
replies
1.5k
views
question using GSEABase
GO GOstats topGO GSEABase GO GOstats topGO GSEABase
updated 15.5 years ago by 25k • written 15.5 years ago by ▴ 80
0
votes
1
reply
1.5k
views
GSEABase GOCollection wrong ontology
Annotation GO hgu133plus2 affy GSEABase Annotation GO hgu133plus2 affy GSEABase
updated 15.7 years ago by 25k • written 15.7 years ago by ▴ 330
0
votes
0
replies
1.5k
views
GSEA to discover co-regulated genes
Transcription Annotation Pathways Infrastructure probe convert GSEABase Transcription
15.8 years ago Paul Geeleher ★ 1.3k
2
votes
2
replies
1.6k
views
GSEA
GSEABase GSEABase
updated 16.0 years ago by 25k • written 16.0 years ago by ★ 1.0k
0
votes
1
reply
1.6k
views
GSEABase
GO illuminaHumanv2 lumi GSEABase GO illuminaHumanv2 lumi GSEABase
updated 16.0 years ago by 25k • written 16.0 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 16.0 years ago by ▴ 90 • written 16.0 years ago by ▴ 830
0
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0
replies
1.3k
views
GSEA packages that depend on GSEABase?
GO GSEABase GO GSEABase
16.3 years ago Mark W Kimpel ▴ 830
0
votes
3
replies
2.6k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
16.3 years ago anna freni sterrantino ▴ 120
0
votes
0
replies
1.3k
views
How to carry out Gene Set Enrichment Analysis(GSEA) on an ordered list of Entrezgene ids?
Proteomics hgu95av2 GSEABase Proteomics hgu95av2 GSEABase
16.3 years ago Chanchal Kumar ▴ 130
0
votes
3
replies
2.0k
views
GeneSetCollection from GSEA
Proteomics GSEABase Proteomics GSEABase
updated 16.7 years ago by 25k • written 16.7 years ago by ▴ 70
0
votes
5
replies
2.4k
views
GSEA and Broad gene sets
Pathways GSEABase Pathways GSEABase
updated 17.0 years ago by ★ 1.2k • written 17.0 years ago by ▴ 30
48 results • Page 1 of 1
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Answer: Handling Epic Array Data by James W. MacDonald 67k
You don't need a sample sheet. It is just a simple way to identify the Idat files and possibly include sample information. But you appear t…
Comment: preprocessIllumina error with EPICv2 array by Rakesh • 0
Amazing, thanks for the help!
Answer: Allele frequencies for ALL alleles of one SNP ? by Robert Castelo ★ 3.4k
Hi, the [GenomicScores](https://bioconductor.org/packages/GenomicSCores) package provides supporting infrastructure to create annotation re…
Answer: preprocessIllumina error with EPICv2 array by James W. MacDonald 67k
You shouldn't need to change the annotation, and certainly not like that. You should never need to use the `@` function directly - there ar…
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by Haibo Liu • 0
Thank you for your reminder. I did forget that, but I just bumped the version to 1.1.1.
Votes
Answer: preprocessIllumina error with EPICv2 array
Answer: preprocessIllumina error with EPICv2 array
Answer: UniProt.ws query loading indefinitely
Answer: Package needs internet access
Answer: Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Ela
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Scholar to James W. MacDonald 67k
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