Showing : enrichment • reset
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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
5
votes
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 4.1 years ago by 50k • written 4.1 years ago by ▴ 60
0
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4
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1.2k
views
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
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
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
2
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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
1
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3
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1.9k
views
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
views
GSVA and ssGSEA output differences
enrichment GSVA enrichplot ssGSEA
updated 2.1 years ago by ★ 3.3k • written 2.1 years ago by • 0
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 11 months ago by ★ 3.9k • written 4.0 years ago by • 0
1
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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
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
2
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2
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889
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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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2
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932
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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
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1
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1.1k
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How to retreive topGO significant IDs of genes after enrichment test ?
topGO significant enrichment genes IDs
5.3 years ago David ROUX ▴ 20
2
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1
reply
1.2k
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Multiple protein ids issue- which protein IDs should be selected for downstream analysis?
Proteomics enrichment Perseus
4.2 years ago harelarik ▴ 60
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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
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0
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873
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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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619
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Over-enrichment of cytobands in INDUCE-Seq
enrichment INDUCE-Seq
2.6 years ago Mark Dunning ★ 1.1k
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522
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Enrichment in genomic regions
Enrichment clusterPro WGCNA
22 months ago María José • 0
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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
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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
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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
22 results • Page 1 of 1
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Comment: package goseq seems to be not available on the latest version of R by Patrycja ▴ 20
limma package also isn't available.Is there any information when these packages will be available?
Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0
Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k
Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…
Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k
For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…
Comment: fgsea significant result by Chris • 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
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