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 16 months ago by ★ 3.9k • written 19 months ago by • 0
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510
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Enrichment in genomic regions
Enrichment clusterPro WGCNA
21 months ago María José • 0
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2
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916
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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 21 months ago by ★ 1.3k • written 21 months ago by • 0
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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 9 weeks ago by • 0 • written 22 months ago by • 0
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3
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5.3k
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GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.0 years ago by ★ 3.2k • written 2.1 years ago by • 0
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609
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Over-enrichment of cytobands in INDUCE-Seq
enrichment INDUCE-Seq
2.5 years ago Mark Dunning ★ 1.1k
2
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2
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874
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Hypergeometric (gene set enrichment) test using "Categories" package
enrichment hypergeometric Categories
2.9 years ago josmantorres ▴ 10
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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 3.4 years ago by 50k • written 3.4 years ago by ▴ 20
4
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4
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1.3k
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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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9.2k
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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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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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4.6k
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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
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7
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2.2k
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Alternative tools to perform GO enrichment on DE genes
go de enrichment rnaseq goana
updated 4.0 years ago by 50k • written 4.0 years ago by ▴ 60
2
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1
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1.2k
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Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
4.1 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
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How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
5.2 years ago David ROUX ▴ 20
2
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3
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952
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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 5.2 years ago by 41k • written 5.2 years ago by ▴ 30
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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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1.2k
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Enrichment of GWAS SNPs in regulatory regions
genomicranges enrichment fisher
7.6 years ago enricoferrero ▴ 660
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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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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
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Answer: Why p value inconsistent when using different number of pathway score? by ATpoint ★ 4.0k
Same answer as here: https://support.bioconductor.org/p/9157606/ Adding or removing data (samples, genes, pathways, observations...) chang…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Thanks Robert!
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Votes
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
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