Showing : gseabase • reset
2
votes
2
replies
707
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase fgsea msigdb GeneSetEnrichment
3 months ago Assa Yeroslaviz ★ 1.5k
0
votes
2
replies
383
views
Problem finding certain variables when importing a public database GSE73103
GSEABase GenomicDistributionsData
7 months ago Yveto • 0
0
votes
1
reply
574
views
"Counts" in enrichGO
GSEABase
updated 10 months ago by ▴ 10 • written 10 months ago by • 0
1
vote
1
reply
1.8k
views
Cleaning GeneSets from GSEA
msigdb GSEABase GSVA
updated 2.7 years ago by ★ 3.4k • written 2.7 years ago by • 0
3
votes
1
reply
1.2k
views
GSEABase::getBroadSets returns error with the latest MSigDB version
GSEABase
updated 4.0 years ago by 25k • written 4.0 years ago by ▴ 60
7
votes
11
replies
3.1k
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
2.2k
views
GSEABase - Map gene/transcript IDs to GOslims?
gseabase go gene ontology goslim
4.8 years ago • updated 21 months ago samwhite ▴ 20
7
votes
9
replies
4.1k
views
GSEABase - View/extract GO terms mapped to each GOslim
go GSEABase GOslim gene ontology
4.8 years ago • updated 21 months ago samwhite ▴ 20
0
votes
3
replies
1.9k
views
GO enrichment for non-model plant species
clusterProfiler GSEABase GMTfiles
5.4 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 25k • written 5.7 years ago by ★ 4.1k
1
vote
1
reply
2.2k
views
Tutorial: Update gene symbols in GeneSetCollection
gseabase msigdb genesetcollection Tutorial
written 6.5 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 6.5 years ago by 43k • written 6.5 years ago by • 0
3
votes
3
replies
1.8k
views
convert Gene collection to gene list for camera function
limma GSEABase
updated 6.8 years ago by 67k • written 6.8 years ago by • 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 7.0 years ago by ★ 3.4k • written 7.0 years ago by ▴ 60
1
vote
2
replies
2.4k
views
RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
gene ontology gseabase
7.3 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
7.9 years ago jcrodriguez ▴ 20
2
votes
2
replies
1.4k
views
Using GeneSetCollection objects of GSEABase in piano package
piano gseabase
7.9 years ago Lluís Revilla Sancho ▴ 760
2
votes
3
replies
1.5k
views
Probable bug in GSEABase package.
software error bug gseabase
7.9 years ago jcrodriguez ▴ 20
1
vote
2
replies
1.7k
views
Question on GeneSetCollection in GSEABase
gseabase geneset
updated 7.9 years ago by 25k • written 7.9 years ago by • 0
1
vote
1
reply
2.0k
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
6.3k
views
GSEA-like enrichment score calculation
GSEA enrichment analysis gseabase
updated 8.5 years ago by 52k • written 8.5 years ago by ▴ 20
0
votes
3
replies
4.4k
views
Creating custom geneset
gseabase
8.9 years ago • updated 8.8 years ago pbachali ▴ 50
8
votes
16
replies
6.2k
views
Gene set enrichment analysis
gostat gsea gseabase topgo
updated 10.1 years ago by ★ 1.1k • written 10.1 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 10.7 years ago by ★ 13k • written 10.7 years ago by ▴ 70
0
votes
5
replies
3.7k
views
Running the GSEA algorithm
Infrastructure PGSEA GSEABase SeqGSEA Infrastructure PGSEA GSEABase SeqGSEA
updated 10.7 years ago by ★ 1.3k • written 10.7 years ago by ▴ 660
0
votes
0
replies
1.2k
views
correlation between two pathways' genes
Microarray Pathways GSEABase Microarray Pathways GSEABase
12.0 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
12.9 years ago Valerie Obenchain ★ 6.8k
0
votes
4
replies
2.3k
views
conversion of geneset species ID
GSEABase GSEABase
updated 13.3 years ago by 25k • written 13.3 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 13.4 years ago by 25k • written 13.4 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
13.8 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 25k • written 14.1 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
14.1 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 14.5 years ago by 25k • written 14.5 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 Gordon Smyth 52k
0
votes
3
replies
1.6k
views
GSEAbase and limma
limma GSEABase limma GSEABase
updated 15.1 years ago by 52k • written 15.1 years ago by ▴ 840
0
votes
3
replies
1.7k
views
GeneSetCollection using EntrezID
Annotation Pathways GSEABase Annotation Pathways GSEABase
updated 15.1 years ago by 25k • written 15.1 years ago by ▴ 840
0
votes
3
replies
1.6k
views
question using GSEABase
GO GOstats topGO GSEABase GO GOstats topGO GSEABase
updated 15.6 years ago by 25k • written 15.6 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 15.8 years ago by 25k • written 15.8 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
15.9 years ago Paul Geeleher ★ 1.3k
2
votes
2
replies
1.6k
views
GSEA
GSEABase GSEABase
updated 16.1 years ago by 25k • written 16.1 years ago by ★ 1.0k
0
votes
1
reply
1.6k
views
GSEABase
GO illuminaHumanv2 lumi GSEABase GO illuminaHumanv2 lumi GSEABase
updated 16.1 years ago by 25k • written 16.1 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 16.1 years ago by ▴ 90 • written 16.1 years ago by ▴ 830
0
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0
replies
1.3k
views
GSEA packages that depend on GSEABase?
GO GSEABase GO GSEABase
16.4 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
16.4 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
16.4 years ago Chanchal Kumar ▴ 130
0
votes
3
replies
2.0k
views
GeneSetCollection from GSEA
Proteomics GSEABase Proteomics GSEABase
updated 16.8 years ago by 25k • written 16.8 years ago by ▴ 70
0
votes
5
replies
2.5k
views
GSEA and Broad gene sets
Pathways GSEABase Pathways GSEABase
updated 17.1 years ago by ★ 1.2k • written 17.1 years ago by ▴ 30
48 results • Page 1 of 1
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Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Hervé Pagès 16k
> I have requested gDNAx developers for a feature request to turn off seqlevelsStyle(txdb) Yes, that's the right course of action. `seqlev…
Comment: ISO a solution to rank-order introns by transcript by mat149 ▴ 80
Hey, In revisiting this question, the following code works for the '+' strand. I am having issues with demarcating intron rank by transcri…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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