https://gregorlueg.r-universe.devRecent package updates in gregorluegR-universehttps://github.com/gregorlueg.pnghttps://gregorlueg.r-universe.devWed, 14 Oct 2026 21:51:11 GMTgregorlueg@me.com (Gregor Lueg)Your favourite methods used in bioinformatics and computational biology made VERY fast via Rust. Contains various gene set enrichment methods, graph- based methods, co-expression module detection and much more. Additionally, has now a single cell analysis suite, enabling million cell scale analysis on local compute.https://github.com/r-universe/gregorlueg/actions/runs/38650407145Wed, 14 Oct 2026 21:51:11 GMTbixverse0.7.0successhttps://gregorlueg.r-universe.devhttps://github.com/GregorLueg/bixversegregorlueg@me.com (Gregor Lueg)Contains different methods to generate embeddings like UMAP, tSNE, DREAMS, PHATE, PacMap and diffusion maps. Morever, has methods to generate nearest neighbour graphs and now also some clustering algorithms that are based on embedding methods (EVoC) and more general clustering methods like k-means.https://github.com/r-universe/gregorlueg/actions/runs/38644746327Wed, 14 Oct 2026 21:11:55 GMTmanifoldsR0.4.0successhttps://gregorlueg.r-universe.devhttps://github.com/GregorLueg/manifoldsRclustering.qmdclustering.htmlClustering methods in manifoldsR2026-04-13 11:05:352026-06-03 08:13:36density_preserving.qmddensity_preserving.htmlDensity-preserving embeddings2026-08-02 13:51:412026-10-03 10:41:02dreams.qmddreams.htmlDREAMS2026-10-14 21:11:552026-10-14 21:11:55knn_searches.qmdknn_searches.htmlNearest neighbour searches2026-03-03 16:41:282026-09-03 08:05:49diffusion_map.qmddiffusion_map.htmlUsing diffusion maps2026-05-08 09:00:102026-05-08 09:00:10fa2.qmdfa2.htmlUsing ForceAtlas22026-09-25 18:17:582026-09-25 18:17:58pacmap.qmdpacmap.htmlUsing PaCMAP2026-03-26 21:29:022026-07-03 16:59:30phate.qmdphate.htmlUsing PHATE2026-03-03 16:41:282026-06-03 08:13:36tsne.qmdtsne.htmlUsing t-SNE2026-03-03 16:41:282026-10-14 21:11:55umap.qmdumap.htmlUsing UMAP2026-03-03 16:41:282026-08-04 12:10:50gregorlueg@me.com (Gregor Lueg)Provides GPU-accelerated methods for the bixverse. These leverage Burn, cubecl and wgpu under the hood to work on very different hardwares.https://github.com/r-universe/gregorlueg/actions/runs/38656464828Sat, 10 Oct 2026 07:24:55 GMTbixverse.gpu0.4.1successhttps://gregorlueg.r-universe.devhttps://github.com/GregorLueg/bixverse.gpugregorlueg@me.com (Gregor Lueg)R interface to the Rust crate 'ann-search-rs'. Build an exact or approximate nearest neighbour index once (HNSW, Annoy, IVF, NNDescent, Vamana and more), keep it in memory behind an R6 object and query it as often as you like. Multi-threaded via Rayon, with f32 or f64 storage.https://github.com/r-universe/gregorlueg/actions/runs/37823222497Thu, 08 Oct 2026 17:56:07 GMTannsearchR0.0.1successhttps://gregorlueg.r-universe.devhttps://github.com/GregorLueg/annsearchRannsearchR.qmdannsearchR.htmlGetting started with annsearchR2026-10-08 17:56:072026-10-08 17:56:07gregorlueg@me.com (Gregor Lueg)Various graph-based methods commonly used in computational biology. Heat diffusions over networks, node2vec and metapath2vec-based analyses over biologicals networks in R powered by Rust. Includes GeneWalkR and co-expression gene drift detection methods based on node2vec.https://github.com/r-universe/gregorlueg/actions/runs/37592682260Wed, 07 Oct 2026 06:01:25 GMTgenewalkR0.2.1successhttps://gregorlueg.r-universe.devhttps://github.com/GregorLueg/genewalkRdiffusion_profiles.qmddiffusion_profiles.htmlDiffusion profiles2026-10-07 06:01:252026-10-07 06:01:25embedding_drift.qmdembedding_drift.htmlEmbedding Drift via node2vec2026-03-09 21:05:462026-05-07 21:40:41diffusion.qmddiffusion.htmlGraph Diffusion2026-04-11 08:14:032026-05-07 21:40:41genewalk.qmdgenewalk.htmlHow to run GeneWalk2026-02-23 20:23:242026-05-07 21:40:41metapath2vec.qmdmetapath2vec.htmlMetapath2vec2026-09-24 12:17:392026-09-24 12:17:39node2vec.qmdnode2vec.htmlNode2vec2026-02-23 20:23:242026-05-07 21:40:41gregorlueg@me.com (Gregor Lueg)Dev-time tooling, not a runtime dependency. Generates the parameter wrapper constructors and their paired checkmate extensions from a declarative spec, and lints the things the house style asks for but cannot enforce: roxygen that has drifted away from the formals it documents, function inputs that never reach a checkmate assertion, and rextendr bindings without an R wrapper.https://github.com/r-universe/gregorlueg/actions/runs/37579071444Tue, 06 Oct 2026 20:37:53 GMTdevforge0.0.7successhttps://gregorlueg.r-universe.devhttps://github.com/GregorLueg/devforgeparams.qmdparams.htmlGenerating parameter wrappers2026-09-17 08:00:192026-09-25 08:15:26gregorlueg@me.com (Gregor Lueg)This package contains various plotting helpers for the core functions of the bixverse package.https://github.com/r-universe/gregorlueg/actions/runs/38656468772Sat, 03 Oct 2026 15:42:29 GMTbixverse.plots0.2.9successhttps://gregorlueg.r-universe.devhttps://github.com/GregorLueg/bixverse.plots