Questions tagged [go-enrichment]

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3answers
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How to convert a list of genes to one element per row?

I got two lists of about 300 genes from my GO analysis, like the following: ...
1
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1answer
35 views

Compare functional enrichment between genelists

I want to compare the results from functional enrichment (e.g GO term enrichment generated by gProfileR) between two gene lists. The idea is to see if these gene lists are enriched in the same terms ...
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2answers
63 views

Alternative to enrichR for enrichment analysis?

I have been using EdgeR to perform differential expression analysis on bulk RNASeq data sets. This analysis gives me an output dataframe that has a list of all the genes, ranked by the their adjP ...
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0answers
46 views

Question about enrichment score (ES) and NES from GSEA

I have two results from separated two GSEA runs, and i want to know which sample has the most enrichment about specific pathway (gene set). Can I use ES (or NES) from two different GSEA analysis ...
4
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1answer
118 views

GOseq analysis with evidence code filter

When using GOseq analysis on RNA-seq data, I often find many 'false positives'. What I mean with that is that some genes in certain categories are not really involved in the process, but are only ...
0
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0answers
121 views

How can I calculate and compare intra-cluster correlation for each GO term and pathway?

How can I calculate and compare intra-cluster correlation for each GO term and pathway? I want for all the genes, which belong to the same GO-term, calculate a similarity score. Each GO term can be ...
3
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2answers
47 views

Is there anything similar to GSEA for locus-based (instead of of gene-based) data?

As the question states, I am interested in an analysis similar to Gene Set Enrichment Analysis (ranked gene sets) but focused on locus-level data instead of genes. To explain in greater detail: I ...
5
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2answers
141 views

Clarification on Gene Enrichment

When I run a GSEA analysis on two conditions from the same RNaseq (negative control PBS injection VS positive control CpG injection) from the same dataset/same gene list, I get results that look ...
4
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2answers
403 views

How to run enrichment analysis of protein functional annotation?

I have a lot of protein clusters. I want to perform an enrichment analysis of their functional annotations, against reference datasets or list of genes I select. More precisely: a method yields ...