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Showing :
enrichment
•
reset
0
votes
0
replies
419
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene
enrichment
topGO
GO
retrieve
11 months ago
Priya
• 0
0
votes
4
replies
1.1k
views
Questions about non-model organisms gene enrichment analysis
non-model
enrichment
organisms
analysis
updated 15 months ago by
Guido Hooiveld
★ 3.9k • written 17 months ago by
yuhang
• 0
0
votes
0
replies
488
views
Enrichment in genomic regions
Enrichment
clusterPro
WGCNA
20 months ago
María José
• 0
0
votes
2
replies
882
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 20 months ago by
swbarnes2
★ 1.3k • written 20 months ago by
ac.mainul.mmb
• 0
1
vote
3
replies
1.7k
views
enrichKEGG results for non-model organism
clusterProfiler
enrichment
KEGG
updated 4 weeks ago by
cinzia.spagnoli
• 0 • written 21 months ago by
AP
• 0
1
vote
3
replies
5.1k
views
GSVA and ssGSEA output differences
enrichment
GSVA
enrichplot
ssGSEA
updated 23 months ago by
Robert Castelo
★ 3.1k • written 23 months ago by
Davide
• 0
0
votes
0
replies
595
views
Over-enrichment of cytobands in INDUCE-Seq
enrichment
INDUCE-Seq
2.5 years ago
Mark Dunning
★ 1.1k
2
votes
2
replies
839
views
Hypergeometric (gene set enrichment) test using "Categories" package
enrichment
hypergeometric
Categories
2.8 years ago
josmantorres
▴ 10
0
votes
7
replies
2.2k
views
topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange
topGO
DifferentialExpression
enrichment
updated 3.4 years ago by
Gordon Smyth
50k • written 3.4 years ago by
lessismore
▴ 20
4
votes
4
replies
1.2k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO
Gene Ontology
enrichment
panther.db
updated 3.5 years ago by
Gordon Smyth
50k • written 3.5 years ago by
Brian Smith
▴ 120
1
vote
2
replies
8.9k
views
Interpreting TSS Enrichment Score Summary
atacseq
atacseqqc
tss
enrichment
updated 3.6 years ago by
Ou, Jianhong
★ 1.3k • written 3.6 years ago by
Arpi Beshlikyan
• 0
0
votes
0
replies
738
views
reactomePA error input file
r
reactomePA
enrichment
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
camillab.
▴ 10
3
votes
3
replies
4.4k
views
Genelist input for ClusterProfiler
R
ClusterProfiler
Enrichment
Pathway
updated 9 months ago by
Guido Hooiveld
★ 3.9k • written 3.9 years ago by
t.b.kuipers
• 0
5
votes
7
replies
2.1k
views
Alternative tools to perform GO enrichment on DE genes
go
de
enrichment
rnaseq
goana
updated 3.9 years ago by
Gordon Smyth
50k • written 3.9 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
4.0 years ago
harelarik
▴ 60
3
votes
3
replies
1.1k
views
Discrepancies between topGO output and input
go
topGO
gene
ontology
enrichment
updated 4.7 years ago by
James W. MacDonald
65k • written 4.7 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
5.1 years ago
David ROUX
▴ 20
2
votes
3
replies
920
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 5.2 years ago by
Michael Love
41k • written 5.2 years ago by
rodrigo.duarte88
▴ 30
0
votes
0
replies
843
views
how to: enrichment (over representation) analysis of GWAS/QTL data distributed over a genome with GOSEQ
goseq
enrichment
GWAS
5.6 years ago
zhu
• 0
0
votes
0
replies
1.1k
views
Enrichment of GWAS SNPs in regulatory regions
genomicranges
enrichment
fisher
7.5 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 9.1 years ago by
belinda.phipson
▴ 40 • written 9.1 years ago by
Ed Schwalbe
▴ 10
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
22 results • Page
1 of 1
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Replies
Comment: DEG Filtering
by
Gordon Smyth
50k
RMA normalization is good but batch correction using NOISeq isn't right. Data shouldn't be batch corrected before the limma analysis and NO…
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…
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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