Package: goat 1.0

goat: Gene Set Analysis Using the Gene Set Ordinal Association Test

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>.

Authors:Frank Koopmans [aut, cre]

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goat.pdf |goat.html✨
goat/json (API)
NEWS

# Install 'goat' in R:
install.packages('goat', repos = c('https://ftwkoopmans.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ftwkoopmans/goat/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:

On CRAN:

bioinformaticsgeneset-enrichmentgeneset-enrichment-analysis

41 exports 6 stars 1.80 score 85 dependencies 8 scripts 951 downloads

Last updated 3 months agofrom:80accdfe5d. Checks:OK: 8 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 21 2024
R-4.5-win-x86_64OKAug 21 2024
R-4.5-linux-x86_64OKAug 21 2024
R-4.4-win-x86_64OKAug 21 2024
R-4.4-mac-x86_64NOTEAug 21 2024
R-4.4-mac-aarch64OKAug 21 2024
R-4.3-win-x86_64OKAug 21 2024
R-4.3-mac-x86_64OKAug 21 2024
R-4.3-mac-aarch64OKAug 21 2024

Exports:cluster_genesetsdarken_colordownload_genesets_goatrepodownload_goat_manuscript_datafilter_genesetsgg_color_huego_gene2gogo_obogoat_logogoat_print_versiongoat_versionhgnc_idmap_tablelighten_colorload_genesets_gmtfileload_genesets_go_bioconductorload_genesets_go_fromfileload_genesets_syngominlog10_fixzeropadjust_genesetspartition_genesplot_heatmapplot_lollipopplot_networkplot_volcanorankscorerankscore_fixed_orderreduce_genesetssave_genesetsscore_geneset_directionalityscore_geneset_oddsratiostring_trunc_rightsymbol_to_entreztest_genesetstest_genesets_fisherexacttest_genesets_goat_bootstraptest_genesets_goat_fitfunctiontest_genesets_goat_precomputedtest_genesets_gseatest_genesets_hypergeometrictreemap_datatreemap_plot

Dependencies:base64encbslibcachemcellrangerclicolorspacecommonmarkcpp11crayondata.tabledigestdplyrfansifarverfastmapfontawesomefsgenericsggforceggplot2ggraphggrepelgluegraphlayoutsgridBasegridExtragtablehmshtmltoolshttpuvigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeMonoPolymunsellnlmepheatmappillarpkgconfigpolyclipprettyunitsprogresspromisespurrrquadprogR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenreadxlrematchrlangsassscalesshinysourcetoolsstringistringrsystemfontstibbletidygraphtidyrtidyselecttreemaptweenrutf8vctrsviridisviridisLitewithrwritexlxtable

Readme and manuals

Help Manual

Help pageTopics
cluster significant genesets from 'test_genesets()' by geneset similarity (separately for each 'geneset source')cluster_genesets
naively darken a color by mixing in blackdarken_color
Download and parse geneset collections from the GOAT GitHub repositorydownload_genesets_goatrepo
Download the datasets that were used in the GOAT manuscriptdownload_goat_manuscript_data
filter a geneset table; intersect with an array of genes-of-interest then apply cutoffs on min/max genes per genesetfilter_genesets
generate colours analogous to ggplot's default palettegg_color_hue
parse gene2go filego_gene2go
simple vectorized parsing of GO OBO file without any dependencies (beyond dplyr/tibble/tidyr)go_obo
ASCII logo for this packagegoat_logo
Precomputed parameters used by the GOAT algorithmgoat_nulldistributions
Print package version and logo to consolegoat_print_version
Return goat package version as a stringgoat_version
Parse HGNC gene identifier lookup table that was downloaded from genenames.org into a table with HGNC ID, symbol, synonym (NA if unavailable), entrez IDhgnc_idmap_table
naively lighten a color by mixing in whitelighten_color
parse genesets in GMT format where gene identifiers are numeric Entrez gene IDsload_genesets_gmtfile
human gene (NCBI entrez ID) annotations from the GO database using the 'org.Hs.eg.db' Bioconductor packageload_genesets_go_bioconductor
construct a geneset table from gene2go and OBO filesload_genesets_go_fromfile
parse genesets from the SynGO databaseload_genesets_syngo
-log10 transform a vector of p-values, replacing zeros with some limit/thresholdminlog10_fixzero
Adjust p-values for all genesets, grouped by 'source' then adjust for the number of 'sources'padjust_genesets
Classify genes into 2 groups, e.g. to define significant or topN genes, resulting in a 'signif' column with boolean valuespartition_genes
plot the geneset similarity matrix as a heatmapplot_heatmap
Lollipop chart or barplot visualization of geneset enrichment testing resultsplot_lollipop
plot geneset distance matrix as a networkplot_network
For each provided geneset, a volcano plot of all genelist log2fc and p-values with respective geneset constituents highlightedplot_volcano
compute rank^2 scores and rescale these between 0~1000 (with further precision captured by decimals)rankscore
Gene score array, from low to high scoresrankscore_fixed_order
Reduce the set of significant genesets to a minimumreduce_genesets
Write a geneset table to file.save_genesets
Compute a score between -1 and 1 representing the proportion of up- or down-regulated genes for each geneset, weighted by gene effectsizesscore_geneset_directionality
Compute odds-ratio for each genesetscore_geneset_oddsratio
simple string truncationstring_trunc_right
Map the the symbol column in a table to HGNC human gene IDs by matching official gene symbols and synonymssymbol_to_entrez
Perform geneset enrichment testing using any supported methodtest_genesets
Geneset ORA using Fisher-exact testtest_genesets_fisherexact
Naive GOAT variant where we estimate null parameters for each geneset size independentlytest_genesets_goat_bootstrap
Variant of the main GOAT function 'test_genesets_goat_precomputed' that does not use previously prepared parameterstest_genesets_goat_fitfunction
Test geneset enrichment with the Geneset Ordinal Association Test (GOAT) algorithmtest_genesets_goat_precomputed
GSEA as implemented in the fgsea R packagetest_genesets_gsea
Geneset ORA using hypergeometric testtest_genesets_hypergeometric
Construct tree and treemap data structures from geneset parent/child relationstreemap_data
Plot a treemaptreemap_plot