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genesetenrichment
•
reset
0
votes
0
replies
278
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
8 months ago
sonal
• 0
0
votes
1
reply
641
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 8 months ago by
James W. MacDonald
65k • written 8 months ago by
manuelsokolov
• 0
0
votes
2
replies
3.0k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
20 months ago
Bhavana
• 0
0
votes
1
reply
781
views
enrichment to common gene
GeneSetEnrichment
genes
genetogo
updated 21 months ago by
Basti
▴ 750 • written 21 months ago by
Noy
• 0
9
votes
13
replies
5.9k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 6 weeks ago by
ATpoint
★ 3.9k • written 2.0 years ago by
nhaus
▴ 10
1
vote
0
replies
1.3k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
2.4 years ago
makrez
▴ 10
3
votes
2
replies
1.2k
views
Self-contained gene set testing with DESeq2 results
roast
DESeq2
GeneSetEnrichment
updated 3.3 years ago by
Gordon Smyth
50k • written 3.3 years ago by
prabin.dm
• 0
0
votes
1
reply
1.3k
views
Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler
GeneSetEnrichment
enrichplot
updated 3.2 years ago by
Emilia
▴ 30 • written 3.3 years ago by
saw44
• 0
0
votes
0
replies
537
views
Clusterprofiler - best practise for missing ids
ReactomePA
clusterProfiler
GeneSetEnrichment
3.3 years ago
paun_bio
• 0
4
votes
3
replies
3.5k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 20 months ago by
pengmin.wang.1
• 0 • written 6.3 years ago by
Huang, Lei [BSD] - CRI
▴ 20
1
vote
4
replies
2.9k
views
Problem retrieving graphics in clusterprofiler
software error
clusterprofiler
GO
genesetenrichment
7.9 years ago
José Luis Lavín
▴ 10
1
vote
0
replies
1.0k
views
performance of limma gene set analysis in relation to Tarca et al. (2013)
limma
genesetenrichment
updated 8.0 years ago by
Steve Lianoglou
★ 13k • written 8.0 years ago by
Aditya
▴ 160
1
vote
0
replies
1.3k
views
News:
Announcing the EnrichmentBrowser 2.0
genesetenrichment
functional enrichment
enrichmentbrowser
News
8.1 years ago
Ludwig Geistlinger
▴ 70
5
votes
7
replies
4.7k
views
Using goseq on non-model organism - how to define genome?
goseq
go
genesetenrichment
updated 8.3 years ago by
Gordon Smyth
50k • written 8.3 years ago by
Jon Bråte
▴ 250
2
votes
1
reply
1.0k
views
elim method for KEGG pathways?
KEGG
genesetenrichment
elim
updated 8.3 years ago by
James W. MacDonald
65k • written 8.3 years ago by
jacorvar
▴ 40
2
votes
2
replies
2.0k
views
Goseq supported organism (felcat5) has an error when testing
goseq
genesetenrichment
annotation
updated 8.6 years ago by
Nadia Davidson
▴ 310 • written 8.6 years ago by
xyliu00
▴ 20
8
votes
14
replies
3.7k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 9.0 years ago by
willem.ligtenberg
▴ 150 • written 9.3 years ago by
Guangchuang Yu
★ 1.2k
1
vote
1
reply
5.2k
views
Reduce the redundancy of enriched GO terms
GO
topgo
genesetenrichment
updated 9.1 years ago by
Luo Weijun
★ 1.6k • written 9.1 years ago by
Alan Smith
▴ 150
0
votes
0
replies
1.1k
views
Using segAnglePo() for a set of genes
geneexpression
genesetenrichment
segAnglePo
9.3 years ago
Peter.Wood
• 0
0
votes
0
replies
1.6k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment
genesetenrichment
dose
gosemsim
9.3 years ago
Guangchuang Yu
★ 1.2k
0
votes
3
replies
1.8k
views
Running the GSEA algorithm
Microarray
GeneSetEnrichment
PGSEA
GSEABase
GSRI
SeqGSEA
Microarray
GeneSetEnrichment
GSRI
updated 10.0 years ago by
Steve Lianoglou
★ 13k • written 10.0 years ago by
Leif Väremo
▴ 70
21 results • Page
1 of 1
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Answer: maftools: Error in validateMaf(maf = maf, isTCGA = isTCGA, rdup = removeDuplicat
by
snijesh
▴ 20
You can try: using `read.delim` or `fread`. ``` my_maf = data.table::fread("path/to/maf/sample.maf") my_maf = read.maf(maf = my_maf) …
Comment: DEG Filtering
by
Amit
• 0
Hi Gordon, Thank you for your response and advice. I want to analyze Dataset GSE18090 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi) whic…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
Gordon Smyth
50k
Yes, that is a quote from [A guide to creating design matrices for gene expression experiments](https://bioconductor.org/packages/release/w…
Comment: edgeR, 3 x 2 design with a batch effect and contrasts
by
JKim
• 0
Thank you. I think I found why the order matters. > Although an intercept-free design matrix has been coded using the 0+ notation, the in…
Comment: Unable to annotate ExpressionSet object from hugene11st chip
by
Efra
• 0
I did as you told, and after running ```eset.annot <- annotateEset(eset, hugene11sttranscriptcluster.db)``` I got the next output: ``` 'se…
Votes
C: How to check that the reads in two fastq files are in the same order
Answer: edgeR, 3 x 2 design with a batch effect and contrasts
Answer: Need help with creating and plotting temporal clustering analysis of DEGs
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
Answer: Problem converting msigdb Human symbols to Zebrafish in gmt format
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