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align=\"center\"\u003e\n  \u003cimg src=\"docs/src/assets/logo.svg\" height=\"250\"\u003e\u003cbr/\u003e\n  \u003ci\u003eRepresenting DNA sequences as regular tetrahedrals (Simplex)\u003c/i\u003e\u003cbr/\u003e\u003cbr/\u003e\n\u003c/div\u003e\n\n\u003cdiv align=\"center\"\u003e\n\n[![Documentation](https://img.shields.io/badge/documentation-online-blue.svg?logo=Julia\u0026logoColor=white)](https://camilogarciabotero.github.io/BioSimplex.jl/dev/)\n[![Latest Release](https://img.shields.io/github/release/camilogarciabotero/BioSimplex.jl.svg)](https://github.com/camilogarciabotero/BioSimplex.jl/releases/latest)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10775955.svg)](https://doi.org/10.5281/zenodo.10775955)\n\u003cbr/\u003e\n[![CI Workflow](https://github.com/camilogarciabotero/BioSimplex.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/camilogarciabotero/BioSimplex.jl/actions/workflows/CI.yml)\n[![License](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/camilogarciabotero/BioSimplex.jl/blob/main/LICENSE)\n[![Work in Progress](https://www.repostatus.org/badges/latest/wip.svg)](https://www.repostatus.org/#wip)\n[![Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/BioSimplex\u0026label=downloads)](https://pkgs.genieframework.com?packages=BioSimplex)\n[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)\n\n\u003c/div\u003e\n\u003c!-- [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10452378.svg)](https://doi.org/10.5281/zenodo.10452378) --\u003e\n\n# BioSimplex\n\n\u003e Representing DNA sequences as regular tetrahedrals (Simplex)\n\nThis packages has a single public function `biosimplex` that takes a `BioSequence` and returns a *Simplex* representation of a *BioSequence*. The *Simplex* representation is a 3D representation of the *BioSequence* where each base can be represented as unit vectors pointing into a regular tetrahedron (Silverman et al., 1986; Coward, 1997).\n\n## Installation\n\n\u003cp\u003e\nBioSimplex is a \u0026nbsp;\n    \u003ca href=\"https://julialang.org\"\u003e\n        \u003cimg src=\"https://raw.githubusercontent.com/JuliaLang/julia-logo-graphics/master/images/julia.ico\" width=\"16em\"\u003e\n        Julia Language\n    \u003c/a\u003e\n    \u0026nbsp; package. To install BioSimplex,\n    please \u003ca href=\"https://docs.julialang.org/en/v1/manual/getting-started/\"\u003eopen\n    Julia's interactive session (known as REPL)\u003c/a\u003e and press \u003ckbd\u003e]\u003c/kbd\u003e\n    key in the REPL to use the package mode, then type the following command\n\u003c/p\u003e\n\n```julia\npkg\u003e add BioSimplex\n```\n\n## Usage\n\n```julia\nusing BioSequences, BioSimplex\n\n# Create a BioSequence\nseq = dna\"ATCG\"\n\n# Convert the BioSequence to a Simplex representation \nbiosimplex(seq)\n\n3×4 Matrix{Float64}:\n 0.0   0.942809  -0.471405  -0.471405\n 0.0   0.0        0.816497  -0.816497\n 1.0  -0.333333  -0.333333  -0.333333\n```\n## Applications\n\nThe *Simplex* representation is useful for to generate a numerical representation of the sequences so that it can be used in machine learning models.\n\n## References\n\nCoward, E. (1997). Equivalence of two Fourier methods for biological sequences. Journal of Mathematical Biology, 36(1), 64–70. https://doi.org/10.1007/s002850050090\n\nSilverman, B. D., \u0026 Linsker, R. (1986). A measure of DNA periodicity. Journal of Theoretical Biology, 118(3), 295–300. https://doi.org/10.1016/S0022-5193(86)80060-1","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcamilogarciabotero%2Fbiosimplex.jl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcamilogarciabotero%2Fbiosimplex.jl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcamilogarciabotero%2Fbiosimplex.jl/lists"}