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goat

INFRA · APIS
Velocity0.0

Gene Set Analysis Using the Gene Set Ordinal Association Test

github.com/ftwkoopmans/goat ↗

A gene-set enrichment package that outgrew its human-only origins, then went quiet.

bioinformaticsgene-set-analysisr-packagecranvisualizationmaintenance
◆Current state
GOAT is a CRAN-published R package for gene set enrichment testing, now at 1.1.4. The visible arc runs from a 2024 beta through a first public CRAN release to a 1.1 line that broadened the package past human gene sets and added persistence for completed analyses. Recent releases are small: the newest ships an igraph handle on plot_network() plus bug fixes.
◆Where it's heading
The substantive expansion happened in the 1.1 cycle; everything since has been maintenance and plotting ergonomics. Each release since 1.1 touches one function and returns something callers previously had to reconstruct, which reads as a package settling into a stable API and responding to individual user requests rather than pursuing new scope. The 13-month gap between 1.1.2 and 1.1.4 puts it firmly in low-cadence maintenance.
◆Prediction
Expect continued point releases that expose internals from the plotting functions or refresh the bundled GO release, not new analysis capability. The entries give no signal of a planned 1.2.

◆Recent moves

  1. 6mo ago

    plot_network() now hands back the igraph object

    plot_network() attaches the underlying igraph object to its return value, so users can restyle or re-layout the network without rebuilding it. A small unblocking change of the kind this package has shipped since 1.1 closed.

    View source ↗
  2. 1y ago

    Fix for a reduce_genesets() infinite loop

    A single edge-case fix where reduce_genesets() could fail to terminate. Correctness work on an already-stable function, with no change to what the package can do.

    View source ↗
  3. 1y ago

    Gene sets beyond human, and analyses you can reload

    ⚡ SPARK

    The release that set the package's current shape: GO gene sets for organisms other than human, plus saved analyses that reload for later plotting. This is the expansion the subsequent 1.1.x maintenance line has been polishing.

    View source ↗
  4. 2y ago

    First public release, now on CRAN

    ⚡ SPARK

    1.0 moves GOAT off a beta line and onto CRAN. It is the point the package became installable and citable by people outside the authors' orbit, and the base the 1.1 expansion built on.

    View source ↗
  5. 2y ago

    plot_lollipop() gains barplots and an effect-size axis

    Pre-CRAN work on the main plotting function: barplot output as an alternative to lollipops, odds ratio on the x-axis instead of -log10 p, and up/down-regulation colour coding. Presentation options rather than new analysis.

    View source ↗
  6. 2y ago

    Beta 0.9.5 tagged, with no changes described

    A beta version stamp with no described changes. The entry marks a point on the pre-1.0 line rather than reporting anything users can act on.

    View source ↗