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Showing :
Enrichment
•
reset
0
votes
0
replies
451
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
12 months ago
Priya
• 0
0
votes
4
replies
1.2k
views
Questions about non-model organisms gene enrichment analysis
non-model
enrichment
organisms
analysis
updated 16 months ago by
Guido Hooiveld
★ 3.9k • written 19 months ago by
yuhang
• 0
0
votes
0
replies
515
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
21 months ago
María José
• 0
0
votes
2
replies
924
views
Seeking help in multifactor differential gene expression analysis using DESeq2. Can not get significance difference while comparing 3 time factor (…
DifferentialExpression
GeneExpression
R
enrichment
DEGseq
updated 22 months ago by
swbarnes2
★ 1.3k • written 22 months ago by
ac.mainul.mmb
• 0
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 10 weeks ago by
cinzia.spagnoli
• 0 • written 22 months ago by
AP
• 0
1
vote
3
replies
5.4k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.1 years ago by
Robert Castelo
★ 3.3k • written 2.1 years ago by
Davide
• 0
0
votes
0
replies
611
views
Over-enrichment of cytobands in INDUCE-Seq
enrichment
INDUCE-Seq
2.6 years ago
Mark Dunning
★ 1.1k
2
votes
2
replies
881
views
Hypergeometric (gene set enrichment) test using "Categories" package
enrichment
hypergeometric
Categories
2.9 years ago
josmantorres
▴ 10
0
votes
7
replies
2.3k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange
topGO
DifferentialExpression
enrichment
updated 3.5 years ago by
Gordon Smyth
50k • written 3.5 years ago by
lessismore
▴ 20
4
votes
4
replies
1.3k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO
Gene Ontology
enrichment
panther.db
updated 3.6 years ago by
Gordon Smyth
50k • written 3.6 years ago by
Brian Smith
▴ 120
1
vote
2
replies
9.2k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 3.7 years ago by
Ou, Jianhong
★ 1.3k • written 3.7 years ago by
Arpi Beshlikyan
• 0
0
votes
0
replies
760
views
reactomePA error input file
r
reactomePA
enrichment
updated 3.9 years ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
camillab.
▴ 10
3
votes
3
replies
4.6k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 10 months ago by
Guido Hooiveld
★ 3.9k • written 4.0 years ago by
t.b.kuipers
• 0
5
votes
7
replies
2.2k
views
Alternative tools to perform GO enrichment on DE genes
go
de
enrichment
rnaseq
goana
updated 4.0 years ago by
Gordon Smyth
50k • written 4.0 years ago by
Raito92
▴ 60
2
votes
1
reply
1.2k
views
Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics
enrichment
Perseus
4.2 years ago • updated 4.1 years ago
harelarik
▴ 60
3
votes
3
replies
1.2k
views
Discrepancies between topGO output and input
go
topGO
gene
ontology
enrichment
updated 4.8 years ago by
James W. MacDonald
65k • written 4.8 years ago by
t.bergmann
• 0
1
vote
1
reply
1.1k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO
significant
enrichment
genes
IDs
5.3 years ago
David ROUX
▴ 20
2
votes
3
replies
959
views
How to calculate overlap between transposable elements differentially expressed in one experiment, with those expressed in another set of samples?
gene expression
enrichment
RNA-seq
DESeq2
updated 5.3 years ago by
Michael Love
41k • written 5.3 years ago by
rodrigo.duarte88
▴ 30
0
votes
0
replies
866
views
how to: enrichment (over representation) analysis of GWAS/QTL data distributed over a genome with GOSEQ
goseq
enrichment
GWAS
5.7 years ago
zhu
• 0
0
votes
0
replies
1.2k
views
Enrichment of GWAS SNPs in regulatory regions
genomicranges
enrichment
fisher
7.6 years ago
enricoferrero
▴ 660
1
vote
2
replies
2.3k
views
Bias correction for enrichment analysis of 450k methylation data => feed bias adjusted genes into IPA
goseq
450k
enrichment
updated 9.2 years ago by
belinda.phipson
▴ 40 • written 9.2 years ago by
Ed Schwalbe
▴ 10
0
votes
0
replies
1.7k
views
DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment
genesetenrichment
dose
gosemsim
9.4 years ago
Guangchuang Yu
★ 1.2k
22 results • Page
1 of 1
Recent ...
Replies
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
pl23
• 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions
by
Michael Love
41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
ussarizona
▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative?
by
Michael Love
41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks
by
ATpoint
★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Votes
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Awards
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to
James W. MacDonald
65k
Popular Question
to
shepherl
3.8k
Scholar
to
Michael Love
41k
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to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
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