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gseabase
•
reset
2
votes
2
replies
752
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
4 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
403
views
Problem finding certain variables when importing a public database GSE73103
GSEABase
GenomicDistributionsData
8 months ago
Yveto
• 0
0
votes
1
reply
615
views
"Counts" in enrichGO
GSEABase
updated 11 months ago by
Tyler Sagendorf
▴ 10 • written 11 months ago by
Matthew
• 0
1
vote
1
reply
1.8k
views
Cleaning GeneSets from GSEA
msigdb
GSEABase
GSVA
updated 2.8 years ago by
Robert Castelo
★ 3.4k • written 2.8 years ago by
forlani.luca
• 0
3
votes
1
reply
1.3k
views
GSEABase::getBroadSets returns error with the latest MSigDB version
GSEABase
updated 4.1 years ago by
Martin Morgan
25k • written 4.1 years ago by
Ezgi
▴ 60
7
votes
11
replies
3.2k
views
Updating Gene Annotation in GeneSetCollection {GSEABase}
GSEABase
annotation
gsea
gsva
GeneSetCollection
updated 4.7 years ago by
Robert Castelo
★ 3.4k • written 4.7 years ago by
rocanja
▴ 60
3
votes
4
replies
2.3k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase
go
gene ontology
goslim
4.9 years ago • updated 22 months ago
samwhite
▴ 20
7
votes
9
replies
4.2k
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
votes
3
replies
1.9k
views
GO enrichment for non-model plant species
clusterProfiler
GSEABase
GMTfiles
5.5 years ago
sandeep.amberkar18
▴ 10
2
votes
2
replies
1.8k
views
GSEABase: how to extract shortDescription from GeneSetCollection object
GSEABase
updated 5.7 years ago by
Martin Morgan
25k • written 5.7 years ago by
Guido Hooiveld
★ 4.1k
1
vote
1
reply
2.2k
views
Tutorial:
Update gene symbols in GeneSetCollection
gseabase
msigdb
genesetcollection
Tutorial
written 6.6 years ago by
t.kuilman
▴ 170
0
votes
3
replies
2.1k
views
Issues in generating workable rank file for GSEA
pre-ranked GSEA
DESeq2
gseabase
GSEA
updated 6.6 years ago by
Michael Love
43k • written 6.6 years ago by
csijst
• 0
3
votes
3
replies
1.9k
views
convert Gene collection to gene list for camera function
limma
GSEABase
updated 6.9 years ago by
James W. MacDonald
67k • written 6.9 years ago by
Seymoo
• 0
2
votes
2
replies
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
Robert Castelo
★ 3.4k • written 7.1 years ago by
rached
▴ 60
1
vote
2
replies
2.5k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology
gseabase
7.4 years ago
maeva.mollion
• 0
0
votes
0
replies
1.2k
views
Does GSEABase support organismDb objects?
GSEABase
7.5 years ago
sandmann.t
▴ 70
0
votes
2
replies
2.1k
views
Problem with GeneSetCollection after updating R devel packages.
bug
gseabase
example
8.0 years ago
jcrodriguez
▴ 20
2
votes
2
replies
1.5k
views
Using GeneSetCollection objects of GSEABase in piano package
piano
gseabase
8.0 years ago
Lluís Revilla Sancho
▴ 760
2
votes
3
replies
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
Martin Morgan
25k • written 8.0 years ago by
siajunren
• 0
1
vote
1
reply
2.0k
views
GSEABase getGmt() fails when more than 1 line contains duplicates
gseabase
bug
updated 8.3 years ago by
Martin Morgan
25k • written 8.3 years ago by
dondelelcaro
▴ 10
9
votes
6
replies
6.3k
views
GSEA-like enrichment score calculation
GSEA
enrichment analysis
gseabase
updated 8.6 years ago by
Gordon Smyth
52k • written 8.6 years ago by
Matthias Z.
▴ 20
0
votes
3
replies
4.4k
views
Creating custom geneset
gseabase
8.9 years ago
pbachali
▴ 50
8
votes
16
replies
6.4k
views
Gene set enrichment analysis
gostat
gsea
gseabase
topgo
updated 10.1 years ago by
Levi Waldron
★ 1.1k • written 10.1 years ago by
kaushal Raj Chaudhary
▴ 10
0
votes
3
replies
2.0k
views
Running the GSEA algorithm
Microarray
GeneSetEnrichment
PGSEA
GSEABase
GSRI
SeqGSEA
Microarray
GeneSetEnrichment
GSRI
updated 10.8 years ago by
Steve Lianoglou
★ 13k • written 10.8 years ago by
Leif Väremo
▴ 70
0
votes
5
replies
3.7k
views
Running the GSEA algorithm
Infrastructure
PGSEA
GSEABase
SeqGSEA
Infrastructure
PGSEA
GSEABase
SeqGSEA
updated 10.8 years ago by
Julian Gehring
★ 1.3k • written 10.8 years ago by
enricoferrero
▴ 660
0
votes
0
replies
1.3k
views
correlation between two pathways' genes
Microarray
Pathways
GSEABase
Microarray
Pathways
GSEABase
12.1 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
13.0 years ago
Valerie Obenchain
★ 6.8k
0
votes
4
replies
2.4k
views
conversion of geneset species ID
GSEABase
GSEABase
updated 13.4 years ago by
Martin Morgan
25k • written 13.4 years ago by
Iain Gallagher
▴ 930
0
votes
1
reply
1.5k
views
creating a UniprotIdentifier within GSEABase
Annotation
Cancer
hgu95av2
convert
GSEABase
Annotation
Cancer
hgu95av2
convert
GSEABase
updated 13.5 years ago by
Martin Morgan
25k • written 13.5 years ago by
Mark Cowley
▴ 910
0
votes
0
replies
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
votes
1
reply
1.9k
views
Help with GSEA package
hu6800
cdf
genefilter
multtest
affy
gcrma
siggenes
annaffy
GSEABase
hu6800
cdf
multtest
updated 14.1 years ago by
Martin Morgan
25k • written 14.1 years ago by
Jillian Rowe
▴ 20
0
votes
0
replies
1.3k
views
creating GO and KEGG gene set collections for E. coli
GO
GSEABase
gage
GO
GSEABase
gage
14.2 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 14.6 years ago by
Martin Morgan
25k • written 14.6 years ago by
Iain Gallagher
▴ 930
0
votes
3
replies
1.9k
views
Romer and symbols2indices query
probe
limma
GSEABase
probe
limma
GSEABase
14.7 years ago
Gordon Smyth
52k
0
votes
3
replies
1.7k
views
GSEAbase and limma
limma
GSEABase
limma
GSEABase
updated 15.2 years ago by
Gordon Smyth
52k • written 15.2 years ago by
Javier Pérez Florido
▴ 840
0
votes
3
replies
1.7k
views
GeneSetCollection using EntrezID
Annotation
Pathways
GSEABase
Annotation
Pathways
GSEABase
updated 15.2 years ago by
Martin Morgan
25k • written 15.2 years ago by
Javier Pérez Florido
▴ 840
0
votes
3
replies
1.6k
views
question using GSEABase
GO
GOstats
topGO
GSEABase
GO
GOstats
topGO
GSEABase
updated 15.7 years ago by
Martin Morgan
25k • written 15.7 years ago by
chunjiang he
▴ 80
0
votes
1
reply
1.5k
views
GSEABase GOCollection wrong ontology
Annotation
GO
hgu133plus2
affy
GSEABase
Annotation
GO
hgu133plus2
affy
GSEABase
updated 15.9 years ago by
Martin Morgan
25k • written 15.9 years ago by
Hans-Ulrich Klein
▴ 330
0
votes
0
replies
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
Martin Morgan
25k • written 16.2 years ago by
Loren Engrav
★ 1.0k
0
votes
1
reply
1.6k
views
GSEABase
GO
illuminaHumanv2
lumi
GSEABase
GO
illuminaHumanv2
lumi
GSEABase
updated 16.2 years ago by
Martin Morgan
25k • written 16.2 years ago by
John Lande
▴ 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 16.2 years ago by
Dykema, Karl
▴ 90 • written 16.2 years ago by
Mark W Kimpel
▴ 830
0
votes
0
replies
1.3k
views
GSEA packages that depend on GSEABase?
GO
GSEABase
GO
GSEABase
16.5 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
16.5 years ago
anna freni sterrantino
▴ 120
0
votes
0
replies
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
votes
3
replies
2.0k
views
GeneSetCollection from GSEA
Proteomics
GSEABase
Proteomics
GSEABase
updated 16.9 years ago by
Martin Morgan
25k • written 16.9 years ago by
Paul ChristophSchröder
▴ 70
0
votes
5
replies
2.5k
views
GSEA and Broad gene sets
Pathways
GSEABase
Pathways
GSEABase
updated 17.1 years ago by
Weiwei Shi
★ 1.2k • written 17.1 years ago by
Brian Hare
▴ 30
48 results • Page
1 of 1
Recent ...
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Comment: Are unequal sample sizes in differential gene expression (DGE) analysis a proble
by
Amora
• 0
Both edgeR and DESeq2 can handle unequal group sizes if you ensure proper quality control and variance estimation. [sprunki retake][1] …
Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
Amora
• 0
You did a great job giving an overview.....[slope][1] better than the bioconductor group! [1]: https://slopeio.org
Comment: contrast matrix design for a continuous variable
by
dtzhu337
• 0
Hi Gordon, Thank you very much for your answer. Actually the variable X is the age, which I am also interested in. Somehow, age and V1 are…
Answer: SingleCellExperiment convenience function for metadata+expression?
by
Peter Hickey
▴ 750
Hi Sarah, `scuttle::makePerCellDF()` / `scuttle::makePerFeatureDF()` and `scater::ggcells()` / `scater::ggfeatures()`, which build upon th…
Comment: How to sort negative log2FC or FC in RNAseq for GSEA?
by
QN
▴ 10
Thank you ATpoint for your response! In the result of GSEA, like you indicated, there will be gene sets that have positive NES and gene se…
Votes
Answer: SingleCellExperiment convenience function for metadata+expression?
How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.
Answer: EdgeR Biological CVs
Answer: Error in download.file for TCGAutils::symbolsToRanges
Answer: Error in download.file for TCGAutils::symbolsToRanges
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