Gene sets enrichment analysis (GSEA) using g:Profiler still works fine for me!

[IngoGiebel]

See https://github.com/IngoGiebel/qbio304-student-work/blob/main/scripts/dge-analysis-PRJCA004229.R on how the variables used here were created,

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Step 5: Gene sets enrichment analysis (GSEA) using g:Profiler

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Oryza nivara

Functional enrichment analysis of the 100 top-ranked genes

top_genes_gostres_onivara <- gprofiler2::gost(
top_genes_onivara_df$geneID[1:100],
organism = "onivara",
correction_method = "fdr")

Produce an interactive manhattan plot of the enriched GO terms

gprofiler2::gostplot(
top_genes_gostres_onivara,
interactive = TRUE,
capped = FALSE)

Produce a static publication quality manhattan plot

with the first 10 top-ranked GO terms highlighted.

gprofiler2::gostplot(
top_genes_gostres_onivara,
interactive = FALSE,
capped = FALSE) |>
gprofiler2::publish_gostplot(
highlight_terms = top_genes_gostres_onivara$result$term_id[1:10])

Generate a table of the gost results of the first 20 top-ranked GO terms

gprofiler2::publish_gosttable(
top_genes_gostres_onivara,
highlight_terms = top_genes_gostres_onivara$result$term_id[1:20],
show_columns = c("source", "term_name", "term_size", "intersection_size"))

Oryza sativa

Functional enrichment analysis of the 100 top-ranked genes

top_genes_gostres_osativa <- gprofiler2::gost(
top_genes_osativa_df$geneID[1:100],
organism = "osativa",
correction_method = "fdr")

Produce an interactive manhattan plot of the enriched GO terms

gprofiler2::gostplot(
top_genes_gostres_osativa,
interactive = TRUE,
capped = FALSE)

Produce a static publication quality manhattan plot

with the first 10 top-ranked GO terms highlighted.

gprofiler2::gostplot(
top_genes_gostres_osativa,
interactive = FALSE,
capped = FALSE) |>
gprofiler2::publish_gostplot(
highlight_terms = top_genes_gostres_osativa$result$term_id[1:10])

Generate a table of the gost results of the first 20 top-ranked GO terms

gprofiler2::publish_gosttable(
top_genes_gostres_osativa,
highlight_terms = top_genes_gostres_osativa$result$term_id[1:20],
show_columns = c("source", "term_name", "term_size", "intersection_size"))