Showing : enrichment • reset
4
votes
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
1
vote
2
replies
9.2k
views
Interpreting TSS Enrichment Score Summary
atacseq atacseqqc tss enrichment
updated 3.7 years ago by ★ 1.3k • written 3.7 years ago by • 0
0
votes
2
replies
924
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 22 months ago by ★ 1.3k • written 22 months ago by • 0
1
vote
3
replies
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
2
votes
3
replies
960
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 5.3 years ago by 41k • written 5.3 years ago by ▴ 30
1
vote
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
3
votes
3
replies
1.2k
views
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
votes
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 • updated 4.1 years ago harelarik ▴ 60
5
votes
7
replies
2.2k
views
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
3
votes
3
replies
4.6k
views
Genelist input for ClusterProfiler
R ClusterProfiler Enrichment Pathway
updated 10 months ago by ★ 3.9k • written 4.0 years ago by • 0
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 9.2 years ago by ▴ 40 • written 9.2 years ago by ▴ 10
2
votes
2
replies
884
views
Hypergeometric (gene set enrichment) test using "Categories" package
enrichment hypergeometric Categories
2.9 years ago josmantorres ▴ 10
0
votes
7
replies
2.3k
views
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
0
votes
4
replies
1.2k
views
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
1
vote
3
replies
1.8k
views
enrichKEGG results for non-model organism
clusterProfiler enrichment KEGG
updated 10 weeks ago by • 0 • written 23 months ago by • 0
0
votes
0
replies
1.2k
views
Enrichment of GWAS SNPs in regulatory regions
genomicranges enrichment fisher
7.6 years ago enricoferrero ▴ 660
0
votes
0
replies
866
views
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
0
votes
0
replies
761
views
reactomePA error input file
r reactomePA enrichment
updated 3.9 years ago by ★ 3.9k • written 3.9 years ago by ▴ 10
0
votes
0
replies
612
views
Over-enrichment of cytobands in INDUCE-Seq
enrichment INDUCE-Seq
2.6 years ago Mark Dunning ★ 1.1k
0
votes
0
replies
515
views
Enrichment in genomic regions
Enrichment clusterPro WGCNA
21 months ago María José • 0
0
votes
0
replies
451
views
topGO: how do I retrieve my genes contributing to the GO term enrichment
gene enrichment topGO GO retrieve
12 months ago Priya • 0
0
votes
0
replies
1.7k
views
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
Recent ...
Replies
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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