Gene Set Analysis Using the Gene Set Ordinal Association Test
Discover available geneset collections from the GOAT GitHub repository
cluster significant genesets from test_genesets() by geneset similar...
naively darken a color by mixing in black
Download and parse geneset collections from the GOAT GitHub repository
Download the datasets that were used in the GOAT manuscript
filter a geneset table; intersect with an array of genes-of-interest t...
generate colours analogous to ggplot's default palette
parse gene2go file
simple vectorized parsing of GO OBO file without any dependencies (bey...
ASCII logo for this package
Print package version and logo to console
Return goat package version as a string
goat: Gene Set Analysis Using the Gene Set Ordinal Association Test
Parse HGNC gene identifier lookup table that was downloaded from genen...
naively lighten a color by mixing in white
parse genesets in GMT format where gene identifiers are numeric Entrez...
Load GO annotations via Bioconductor packages (e.g. org.Hs.eg.db for H...
construct a geneset table from gene2go and OBO files
parse genesets from the SynGO database
-log10 transform a vector of p-values, replacing zeros with some limit...
Adjust p-values for all genesets, grouped by 'source' then adjust for ...
Classify genes into 2 groups, e.g. to define significant or topN genes...
plot the geneset similarity matrix as a heatmap
Lollipop chart or barplot visualization of geneset enrichment testing ...
plot geneset distance matrix as a network
For each provided geneset, a volcano plot of all genelist log2fc and p...
Gene score array, from low to high scores
compute rank^2 scores and rescale these between 0~1000 (with further p...
Reduce the set of significant genesets to a minimum
Write a geneset table to file.
Compute a score between -1 and 1 representing the proportion of up- or...
Compute odds-ratio for each geneset
simple string truncation
Map the the symbol column in a table to HGNC human gene IDs by matchin...
Lookup table for taxonomy identifiers, their names and respective Bioc...
Geneset ORA using Fisher-exact test
Naive GOAT variant where we estimate null parameters for each geneset ...
Variant of the main GOAT function test_genesets_goat_precomputed tha...
Test geneset enrichment with the Geneset Ordinal Association Test (GOA...
GSEA as implemented in the fgsea R package
Geneset ORA using hypergeometric test
Perform geneset enrichment testing using any supported method
Construct tree and treemap data structures from geneset parent/child r...
Plot a treemap
Perform gene set enrichment analyses using the Gene set Ordinal Association Test (GOAT) algorithm and visualize your results. Koopmans, F. (2024) <doi:10.1038/s42003-024-06454-5>.