https://github.com/camilogarciabotero/biosimplex.jl
Representing BioSequences as Simplex numerical matrix
Science Score: 46.0%
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Keywords
Repository
Representing BioSequences as Simplex numerical matrix
Basic Info
- Host: GitHub
- Owner: camilogarciabotero
- License: mit
- Language: Julia
- Default Branch: main
- Homepage: https://camilogarciabotero.github.io/BioSimplex.jl/
- Size: 145 KB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 2
Topics
Metadata Files
README.md
Representing DNA sequences as regular tetrahedrals (Simplex)
[](https://github.com/camilogarciabotero/BioSimplex.jl/actions/workflows/CI.yml) [](https://github.com/camilogarciabotero/BioSimplex.jl/blob/main/LICENSE) [](https://www.repostatus.org/#wip) [](https://pkgs.genieframework.com?packages=BioSimplex) [](https://github.com/JuliaTesting/Aqua.jl)
BioSimplex
Representing DNA sequences as regular tetrahedrals (Simplex)
This 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).
Installation
BioSimplex is a
julia
pkg> add BioSimplex
Usage
```julia using BioSequences, BioSimplex
Create a BioSequence
seq = dna"ATCG"
Convert the BioSequence to a Simplex representation
biosimplex(seq)
3×4 Matrix{Float64}: 0.0 0.942809 -0.471405 -0.471405 0.0 0.0 0.816497 -0.816497 1.0 -0.333333 -0.333333 -0.333333 ```
Applications
The Simplex representation is useful for to generate a numerical representation of the sequences so that it can be used in machine learning models.
References
Coward, E. (1997). Equivalence of two Fourier methods for biological sequences. Journal of Mathematical Biology, 36(1), 64–70. https://doi.org/10.1007/s002850050090
Silverman, B. D., & 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
Owner
- Name: Camilo García
- Login: camilogarciabotero
- Kind: user
- Location: Bogotá, Colombia
- Company: Universidad de los Andes
- Website: https://camilogarciabotero.github.io
- Twitter: gaspardelanoche
- Repositories: 8
- Profile: https://github.com/camilogarciabotero
Biologist interested in applying bioinformatics and DS tools to understand evolution in different organisms. Currently working on bacteriophages and epigenomics
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| Name | Commits | |
|---|---|---|
| Camilo García | c****2@u****o | 21 |
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