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Showing :
Enrichment
•
reset
0
votes
0
replies
517
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
15 months ago
Priya
• 0
0
votes
4
replies
1.3k
views
Questions about non-model organisms gene enrichment analysis
non-model
enrichment
organisms
analysis
updated 19 months ago by
Guido Hooiveld
★ 4.0k • written 22 months ago by
yuhang
• 0
0
votes
0
replies
565
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
2.1 years ago
María José
• 0
0
votes
2
replies
997
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 2.1 years ago by
swbarnes2
★ 1.4k • written 2.1 years ago by
ac.mainul.mmb
• 0
1
vote
3
replies
2.1k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 5 months ago by
cinzia.spagnoli
• 0 • written 2.1 years ago by
AP
• 0
1
vote
3
replies
6.2k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 2.3 years ago by
Robert Castelo
★ 3.3k • written 2.3 years ago by
Davide
• 0
0
votes
0
replies
662
views
Over-enrichment of cytobands in INDUCE-Seq
enrichment
INDUCE-Seq
2.8 years ago
Mark Dunning
★ 1.1k
2
votes
2
replies
934
views
Hypergeometric (gene set enrichment) test using "Categories" package
enrichment
hypergeometric
Categories
3.2 years ago
josmantorres
▴ 10
0
votes
7
replies
2.6k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange
topGO
DifferentialExpression
enrichment
updated 3.7 years ago by
Gordon Smyth
51k • written 3.7 years ago by
lessismore
▴ 20
4
votes
4
replies
1.4k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO
Gene Ontology
enrichment
panther.db
updated 3.9 years ago by
Gordon Smyth
51k • written 3.9 years ago by
Brian Smith
▴ 120
1
vote
2
replies
9.9k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 3.9 years ago by
Ou, Jianhong
★ 1.3k • written 4.0 years ago by
Arpi Beshlikyan
• 0
0
votes
0
replies
834
views
reactomePA error input file
r
reactomePA
enrichment
updated 4.1 years ago by
Kevin Blighe
★ 4.0k • written 4.1 years ago by
camillab.
▴ 10
3
votes
3
replies
5.2k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 13 months ago by
Guido Hooiveld
★ 4.0k • written 4.3 years ago by
t.b.kuipers
• 0
5
votes
7
replies
2.4k
views
Alternative tools to perform GO enrichment on DE genes
go
de
enrichment
rnaseq
goana
updated 4.3 years ago by
Gordon Smyth
51k • written 4.3 years ago by
Raito92
▴ 60
2
votes
1
reply
1.4k
views
Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics
enrichment
Perseus
4.4 years ago
harelarik
▴ 60
3
votes
3
replies
1.3k
views
Discrepancies between topGO output and input
go
topGO
gene
ontology
enrichment
updated 5.1 years ago by
James W. MacDonald
66k • written 5.1 years ago by
t.bergmann
• 0
1
vote
1
reply
1.2k
views
How to retreive topGO significant IDs of genes after enrichment test ?
topGO
significant
enrichment
genes
IDs
5.5 years ago
David ROUX
▴ 20
2
votes
3
replies
1.1k
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 5.5 years ago by
Michael Love
42k • written 5.5 years ago by
rodrigo.duarte88
▴ 40
0
votes
0
replies
935
views
how to: enrichment (over representation) analysis of GWAS/QTL data distributed over a genome with GOSEQ
goseq
enrichment
GWAS
5.9 years ago
zhu
• 0
0
votes
0
replies
1.2k
views
Enrichment of GWAS SNPs in regulatory regions
genomicranges
enrichment
fisher
7.8 years ago
enricoferrero
▴ 660
1
vote
2
replies
2.4k
views
Bias correction for enrichment analysis of 450k methylation data => feed bias adjusted genes into IPA
goseq
450k
enrichment
updated 9.4 years ago by
belinda.phipson
▴ 40 • written 9.4 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
9.7 years ago
Guangchuang Yu
★ 1.2k
22 results • Page
1 of 1
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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to
Lluís Revilla Sancho
▴ 730
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to
maltethodberg
▴ 180
Scholar
to
Michael Love
42k
Popular Question
to
Leonardo Collado Torres
★ 1.1k
Scholar
to
Gordon Smyth
51k
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