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genesetenrichment
•
reset
0
votes
0
replies
433
views
fgsea: ranking genes using log2FC and pvalues derived from spline model
fgsea
GeneSetEnrichment
splines
RNASeq
7 months ago
GT
• 0
0
votes
0
replies
301
views
News:
GSEA in R/Bioconductor course
GSEABenchmarkeR
pairedGSEA
GeneSetEnrichment
7 months ago
info
▴ 10
0
votes
2
replies
645
views
cameraPR() non directional test
CAMERA
GeneSetEnrichment
8 months ago • updated 7 months ago
Hugo Varet
▴ 80
0
votes
1
reply
686
views
News:
Gene Set Enrichment Analysis in Bioconductor course
GSEABase
GeneSetEnrichment
goseq
8 months ago • updated 7 months ago
info
▴ 10
0
votes
1
reply
368
views
Comparing Mock vs Infected in WT and Knockout Cells
DESeq2
DifferentialExpression
DifferentialRegulation
RNASeq
GeneSetEnrichment
updated 8 months ago by
Michael Love
43k • written 8 months ago by
Sahil
• 0
2
votes
2
replies
1.2k
views
fgsea stuck in an infinite loop in the middle of the run
GSEABase
fgsea
msigdb
GeneSetEnrichment
13 months ago
Assa Yeroslaviz
★ 1.5k
0
votes
1
reply
1.1k
views
How to rank DEG for GSEA using DEseq2 result ?
DESeq2
limma
GeneSetEnrichment
updated 15 months ago by
ATpoint
★ 5.0k • written 15 months ago by
picasa1983
• 0
0
votes
1
reply
1.4k
views
Gene set enrichment analysis
clusterProfiler
GeneSetEnrichment
updated 17 months ago by
Guido Hooiveld
★ 4.1k • written 17 months ago by
aogunbaw
• 0
1
vote
2
replies
2.5k
views
geneList error in clusterprofiler
clusterProfiler
GeneSetEnrichment
18 months ago
Ana
• 0
0
votes
2
replies
996
views
How to make GSEAplot with chip set
geneset
GeneSetEnrichment
msigdb
18 months ago
Seongsu
• 0
4
votes
4
replies
5.1k
views
Function simplify fails when argument ont is set to "ALL" in enrichGO function in package clusterProfiler
clusterProfiler
GO
GO enrichment
genesetenrichment
updated 19 months ago by
jandrade
• 0 • written 7.8 years ago by
Huang, Lei [BSD] - CRI
▴ 20
0
votes
0
replies
786
views
BubbleGUM for multi group comparison of gene set enrichment
RNASeqData
GeneSetEnrichment
multiGSEA
2.3 years ago
sonal
• 0
0
votes
1
reply
2.1k
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
gseGO
GeneSet
clusterProfiler
GeneSetEnrichment
updated 2.3 years ago by
James W. MacDonald
68k • written 2.3 years ago by
manuelsokolov
• 0
0
votes
2
replies
6.0k
views
What is the significance of "Zero Cross" in Ranked List Metric in Gene Set Enrichment Analysis ?
GSEA
GeneSetEnrichment
3.3 years ago
Bhavana
• 0
0
votes
1
reply
1.7k
views
enrichment to common gene
GeneSetEnrichment
genes
genetogo
updated 3.4 years ago by
Basti
▴ 780 • written 3.4 years ago by
Noy
• 0
12
votes
13
replies
13k
views
GSEA many significant gene sets despite no differentially expressed genes
GSEA
GeneSetEnrichment
DifferentialExpression
updated 20 months ago by
ATpoint
★ 5.0k • written 3.6 years ago by
nhaus
▴ 70
1
vote
0
replies
2.1k
views
GSEA using clusterProfiler with non-model organism.
clusterProfiler
KEGG
GeneSetEnrichment
4.0 years ago
makrez
▴ 10
3
votes
2
replies
1.9k
views
Self-contained gene set testing with DESeq2 results
roast
DESeq2
GeneSetEnrichment
updated 4.8 years ago by
Gordon Smyth
53k • written 4.8 years ago by
prabin.dm
• 0
0
votes
1
reply
1.9k
views
Cut down genes displayed on x axis from enrichPlot's heatplot() function
clusterProfiler
GeneSetEnrichment
enrichplot
updated 4.8 years ago by
Emilia
▴ 40 • written 4.9 years ago by
saw44
• 0
0
votes
0
replies
863
views
Clusterprofiler - best practise for missing ids
ReactomePA
clusterProfiler
GeneSetEnrichment
4.9 years ago
paun_bio
• 0
1
vote
4
replies
3.8k
views
Problem retrieving graphics in clusterprofiler
software error
clusterprofiler
GO
genesetenrichment
9.5 years ago
José Luis Lavín
▴ 10
1
vote
0
replies
1.4k
views
performance of limma gene set analysis in relation to Tarca et al. (2013)
limma
genesetenrichment
updated 9.6 years ago by
Steve Lianoglou
★ 13k • written 9.6 years ago by
Aditya
▴ 160
1
vote
0
replies
1.7k
views
News:
Announcing the EnrichmentBrowser 2.0
genesetenrichment
functional enrichment
enrichmentbrowser
News
9.7 years ago
Ludwig Geistlinger
▴ 70
5
votes
7
replies
6.0k
views
Using goseq on non-model organism - how to define genome?
goseq
go
genesetenrichment
updated 9.8 years ago by
Gordon Smyth
53k • written 9.8 years ago by
Jon Bråte
▴ 270
2
votes
1
reply
1.3k
views
elim method for KEGG pathways?
KEGG
genesetenrichment
elim
updated 9.9 years ago by
James W. MacDonald
68k • written 9.9 years ago by
jacorvar
▴ 40
2
votes
2
replies
2.4k
views
Goseq supported organism (felcat5) has an error when testing
goseq
genesetenrichment
annotation
updated 10.2 years ago by
Nadia Davidson
▴ 320 • written 10.2 years ago by
xyliu00
▴ 20
8
votes
14
replies
5.1k
views
reactome.db is not updated?
genesetenrichment
pathways
reactome.db
updated 10.5 years ago by
willem.ligtenberg
▴ 150 • written 10.9 years ago by
Guangchuang Yu
★ 1.2k
1
vote
1
reply
6.0k
views
Reduce the redundancy of enriched GO terms
GO
topgo
genesetenrichment
updated 10.7 years ago by
Luo Weijun
★ 1.6k • written 10.7 years ago by
Alan Smith
▴ 150
0
votes
0
replies
1.4k
views
Using segAnglePo() for a set of genes
geneexpression
genesetenrichment
segAnglePo
10.8 years ago
Peter.Wood
• 0
0
votes
0
replies
2.1k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment
genesetenrichment
dose
gosemsim
10.9 years ago
Guangchuang Yu
★ 1.2k
0
votes
3
replies
2.3k
views
Running the GSEA algorithm
Microarray
GeneSetEnrichment
PGSEA
GSEABase
GSRI
SeqGSEA
Microarray
GeneSetEnrichment
GSRI
updated 11.6 years ago by
Steve Lianoglou
★ 13k • written 11.6 years ago by
Leif Väremo
▴ 70
31 results • Page
1 of 1
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Comment: Announcing GBCC 2025: The first-ever joint conference between Bioconductor and G
by
dzv20413
• 0
Wow, GBCC 2025 sounds amazing, can not wait to see the logo contest results! Also, I just played [Level Devil][1] and it is super addictive…
Comment: Memory error while running alignments
by
Erik Wright
▴ 150
How much memory is available on the computer? A distance matrix of 50k sequences requires at least 50k*50k/2 * 8 bytes = 10GB, assuming the…
Comment: NA values for DESeq2 p-values and adjusted p-values using large sample sizes
by
Gabriel
• 0
Thank you very much for the reply. However, none of these three options seems to fit: 1) The genes for which NA appears do not have all 0 …
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames
by
ubjw24
• 0
Thank you for your replies. I got the problem solved by installing mutSignature with this line: ``` devtools::install_github("dami82/mutS…
Comment: DESeq2 design for haplotype MPRA
by
Rita
• 0
Thank you very much, I appreciate it!
Votes
Comment: Check removeBatchEffect effectiveness
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset?
Answer: DESeq2 design for haplotype MPRA
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
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Gordon Smyth
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