Showing : enrichment • reset
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topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
12 months ago Priya • 0
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4
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1.2k
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Questions about non-model organisms gene enrichment analysis
non-model enrichment organisms analysis
updated 17 months ago by ★ 3.9k • written 19 months ago by • 0
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521
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Enrichment in genomic regions
Enrichment clusterPro WGCNA
22 months ago María José • 0
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2
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931
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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 ★ 1.3k • written 22 months ago by • 0
1
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3
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1.8k
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enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 11 weeks ago by • 0 • written 23 months ago by • 0
1
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3
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5.4k
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GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.1 years ago by ★ 3.3k • written 2.1 years ago by • 0
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0
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618
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Over-enrichment of cytobands in INDUCE-Seq
enrichment INDUCE-Seq
2.6 years ago Mark Dunning ★ 1.1k
2
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2
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888
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Hypergeometric (gene set enrichment) test using "Categories" package
enrichment hypergeometric Categories
3.0 years ago josmantorres ▴ 10
0
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7
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2.3k
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topGO: GO term enrichment analysis of differentially expressed genes (!) including fold-change (!)
foldchange topGO DifferentialExpression enrichment
updated 3.5 years ago by 50k • written 3.5 years ago by ▴ 20
4
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4
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1.3k
views
Replicating GO website analysis with bioconductor packages (topGO?)
topGO Gene Ontology enrichment panther.db
updated 3.6 years ago by 50k • written 3.6 years ago by ▴ 120
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2
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9.3k
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Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
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0
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770
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reactomePA error input file
r reactomePA enrichment
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
3
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3
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4.7k
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Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
5
votes
7
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2.2k
views
Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 4.1 years ago by 50k • written 4.1 years ago by ▴ 60
2
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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 harelarik ▴ 60
3
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3
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1.2k
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Discrepancies between topGO output and input
go topGO gene ontology enrichment
updated 4.8 years ago by 65k • written 4.8 years ago by • 0
1
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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
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968
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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 41k • written 5.3 years ago by ▴ 30
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872
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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
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0
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1.2k
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Enrichment of GWAS SNPs in regulatory regions
genomicranges enrichment fisher
7.6 years ago enricoferrero ▴ 660
1
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2
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2.3k
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Bias correction for enrichment analysis of 450k methylation data => feed bias adjusted genes into IPA
goseq 450k enrichment
updated 9.2 years ago by ▴ 40 • written 9.2 years ago by ▴ 10
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0
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1.7k
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DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis
enrichment genesetenrichment dose gosemsim
9.5 years ago Guangchuang Yu ★ 1.2k
22 results • Page 1 of 1
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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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