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bixverse - Rust-accelerated standard bioinformatics, computational biology workflows

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.

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bioinformaticscomputational-biologyr-languagesingle-cellrustcargo

6.70 score 37 stars 2 dependents 54 scripts

genewalkR - Graph-based computational algorithms in R, including diffusions and small neural networks like node2vec.

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.

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bioinformaticscomputational-biologydeep-learningnetwork-analysisnode2vecrustcargoquarto

5.12 score 2 stars 7 scripts

manifoldsR - Fast Low-Dimensional Embeddings and Clustering via 'Rust'

R interface to the Rust crates 'manifolds-rs', 'ann-search-rs' and 'evoc-rs'. Builds 2D (or higher) embeddings with UMAP (McInnes et al., 2018) <doi:10.48550/arXiv.1802.03426>, t-SNE (van der Maaten and Hinton, 2008) <https://jmlr.org/papers/v9/vandermaaten08a.html>, densMAP and den-SNE (Narayan et al., 2021) <doi:10.1038/s41587-020-00801-7>, PHATE (Moon et al., 2019) <doi:10.1038/s41587-019-0336-3>, PaCMAP (Wang et al., 2021) <https://jmlr.org/papers/v22/20-1061.html>, ForceAtlas2 (Jacomy et al., 2014) <doi:10.1371/journal.pone.0098679>, DREAMS and diffusion maps. Also generates approximate nearest neighbour graphs that every method can reuse, plus EVoC and k-means clustering. Multi-threaded via 'Rayon', with f32 or f64 precision.

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phaterustsingle-celltsneumapcargo

4.26 score 2 stars 3 dependents

devforge - Development tooling for the bixverse family of R packages

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.

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quarto

3.30 score

annsearchR - Fast Approximate Nearest Neighbour Search

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. Methods include hierarchical navigable small world graphs (Malkov and Yashunin, 2020) <doi:10.1109/TPAMI.2018.2889473> and NN-Descent (Dong, Charikar and Li, 2011) <doi:10.1145/1963405.1963487>.

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rustcargoquarto

3.00 score

bixverse.gpu - GPU-accelerated methods via cubecl and WGPU for the bixverse with general methods such as k-means and correlations and a lot of methods specific for single cell analysis acceleration.

Provides GPU-accelerated methods for the bixverse. These leverage Burn, cubecl and wgpu under the hood to work on very different hardwares.

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computational-biologygpur-languagesingle-cellrustcargo

2.90 score 1 stars 1 scripts

bixverse.plots - Plotting functions for bixverse

This package contains various plotting helpers for the core functions of the bixverse package.

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bioinformaticsggplot2

2.80 score 14 scripts