Man pages for goat
Gene Set Analysis Using the Gene Set Ordinal Association Test
| available_genesets_goatrepo | Discover available geneset collections from the GOAT GitHub... |
| cluster_genesets | cluster significant genesets from 'test_genesets()' by... |
| darken_color | naively darken a color by mixing in black |
| download_genesets_goatrepo | Download and parse geneset collections from the GOAT GitHub... |
| download_goat_manuscript_data | Download the datasets that were used in the GOAT manuscript |
| filter_genesets | filter a geneset table; intersect with an array of... |
| gg_color_hue | generate colours analogous to ggplot's default palette |
| goat | goat: Gene Set Analysis Using the Gene Set Ordinal... |
| goat_logo | ASCII logo for this package |
| goat_nulldistributions | Precomputed parameters used by the GOAT algorithm |
| goat_print_version | Print package version and logo to console |
| goat_version | Return goat package version as a string |
| go_gene2go | parse gene2go file |
| go_obo | simple vectorized parsing of GO OBO file without any... |
| hgnc_idmap_table | Parse HGNC gene identifier lookup table that was downloaded... |
| lighten_color | naively lighten a color by mixing in white |
| load_genesets_gmtfile | parse genesets in GMT format where gene identifiers are... |
| load_genesets_go_bioconductor | Load GO annotations via Bioconductor packages (e.g.... |
| load_genesets_go_fromfile | construct a geneset table from gene2go and OBO files |
| load_genesets_syngo | parse genesets from the SynGO database |
| minlog10_fixzero | -log10 transform a vector of p-values, replacing zeros with... |
| padjust_genesets | Adjust p-values for all genesets, grouped by 'source' then... |
| partition_genes | Classify genes into 2 groups, e.g. to define significant or... |
| plot_heatmap | plot the geneset similarity matrix as a heatmap |
| plot_lollipop | Lollipop chart or barplot visualization of geneset enrichment... |
| plot_network | plot geneset distance matrix as a network |
| plot_volcano | For each provided geneset, a volcano plot of all genelist... |
| rankscore | compute rank^2 scores and rescale these between 0~1000 (with... |
| rankscore_fixed_order | Gene score array, from low to high scores |
| reduce_genesets | Reduce the set of significant genesets to a minimum |
| save_genesets | Write a geneset table to file. |
| score_geneset_directionality | Compute a score between -1 and 1 representing the proportion... |
| score_geneset_oddsratio | Compute odds-ratio for each geneset |
| string_trunc_right | simple string truncation |
| symbol_to_entrez | Map the the symbol column in a table to HGNC human gene IDs... |
| taxonomy_identifiers | Lookup table for taxonomy identifiers, their names and... |
| test_genesets | Perform geneset enrichment testing using any supported method |
| test_genesets_fisherexact | Geneset ORA using Fisher-exact test |
| test_genesets_goat_bootstrap | Naive GOAT variant where we estimate null parameters for each... |
| test_genesets_goat_fitfunction | Variant of the main GOAT function... |
| test_genesets_goat_precomputed | Test geneset enrichment with the Geneset Ordinal Association... |
| test_genesets_gsea | GSEA as implemented in the fgsea R package |
| test_genesets_hypergeometric | Geneset ORA using hypergeometric test |
| treemap_data | Construct tree and treemap data structures from geneset... |
| treemap_plot | Plot a treemap |
