[//]: # (# CodonU)
[](https://opensource.org/licenses/MIT)
[](https://pepy.tech/project/codonu)
[](https://www.codefactor.io/repository/github/souradiptoc/codonu/overview/master)
[](https://souradiptoc.github.io/CodonU/)
# Introduction
Welcome to CodonU!
This is an integrated package for codon usage analysis.
# Functionalities
Various functionalities can be found below. For gene/genome analysis, this package can:
- For Nucleotide sequences
- Calculate RSCU
- Calculate CAI
- Calculate CBI
- Calculate ENc
- For Protein sequences
- Calculate Aromaticity
- Calculate gravy
One can also can calculate the multivariate analysis, popularly known as correspondence analysis (COA) for the codons
easily.
Supported calculations are:
- For Nucleotide sequences
- COA using codon frequency with scale set to length of gene
- COA using codon RSCU values with scale set to length of gene
- For Protein sequences
- COA using amino acid frequency with scale set to gravy score
- COA using amino acid frequency with scale set to aromaticity score
Phylogenetic analysis and tree building now can be done.
Detailed instructions on how to use the functions can be found in
the [examples](https://github.com/SouradiptoC/CodonU/tree/master/Examples)
# Installation
pip install CodonU
# Future Plans
None. If you would like recommend one, please mail
at [sourochaudhuri@gmail.com](mailto:sourochaudhuri@gmail.com)
Raw data
{
"_id": null,
"home_page": "https://github.com/SouradiptoC/codon_usage",
"name": "CodonU",
"maintainer": "",
"docs_url": null,
"requires_python": "",
"maintainer_email": "",
"keywords": "bioinformatics,bioinformatics-analysis,bioinformatics-tool,codon-usage,codon,codon-bias,genomic-analysis,genome,codonW",
"author": "Souradipto Choudhuri",
"author_email": "sourochaudhuri@gmail.com",
"download_url": "https://files.pythonhosted.org/packages/18/23/e28f322c06ce1794ed29acc087ef810e45b10185f5102838fbbc91399c1a/CodonU-1.0.2.tar.gz",
"platform": null,
"description": "[//]: # (# CodonU)\n\n[](https://opensource.org/licenses/MIT)\n[](https://pepy.tech/project/codonu)\n[](https://www.codefactor.io/repository/github/souradiptoc/codonu/overview/master)\n[](https://souradiptoc.github.io/CodonU/)\n\n# Introduction\n\nWelcome to CodonU!\n\nThis is an integrated package for codon usage analysis.\n\n# Functionalities\n\nVarious functionalities can be found below. For gene/genome analysis, this package can:\n\n- For Nucleotide sequences\n - Calculate RSCU\n - Calculate CAI\n - Calculate CBI\n - Calculate ENc\n- For Protein sequences\n - Calculate Aromaticity\n - Calculate gravy\n\nOne can also can calculate the multivariate analysis, popularly known as correspondence analysis (COA) for the codons\neasily.\nSupported calculations are:\n\n- For Nucleotide sequences\n - COA using codon frequency with scale set to length of gene\n - COA using codon RSCU values with scale set to length of gene\n- For Protein sequences\n - COA using amino acid frequency with scale set to gravy score\n - COA using amino acid frequency with scale set to aromaticity score\n\nPhylogenetic analysis and tree building now can be done.\n\nDetailed instructions on how to use the functions can be found in\nthe [examples](https://github.com/SouradiptoC/CodonU/tree/master/Examples)\n\n# Installation\n\n pip install CodonU\n\n# Future Plans\n\nNone. If you would like recommend one, please mail\nat [sourochaudhuri@gmail.com](mailto:sourochaudhuri@gmail.com)\n",
"bugtrack_url": null,
"license": "MIT License",
"summary": "This package is designed for helping in genomic analysis",
"version": "1.0.2",
"split_keywords": [
"bioinformatics",
"bioinformatics-analysis",
"bioinformatics-tool",
"codon-usage",
"codon",
"codon-bias",
"genomic-analysis",
"genome",
"codonw"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "f4b88cafb3c1980a3a5b725ca6acbf4a5b0bf95b28d36f15551c7855a7d9d00e",
"md5": "be702d7e56c9be12576526948aa825e6",
"sha256": "9d8334b43847a8d08b2cb06a233d7c2d905c0a2b95770873ee50df2ba184404f"
},
"downloads": -1,
"filename": "CodonU-1.0.2-py3-none-any.whl",
"has_sig": false,
"md5_digest": "be702d7e56c9be12576526948aa825e6",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": null,
"size": 45897,
"upload_time": "2023-04-24T07:20:18",
"upload_time_iso_8601": "2023-04-24T07:20:18.418627Z",
"url": "https://files.pythonhosted.org/packages/f4/b8/8cafb3c1980a3a5b725ca6acbf4a5b0bf95b28d36f15551c7855a7d9d00e/CodonU-1.0.2-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "1823e28f322c06ce1794ed29acc087ef810e45b10185f5102838fbbc91399c1a",
"md5": "07f1a816b3335d8c1b8c9ea88ceefe0d",
"sha256": "6dbd99259d2110ef44d54a3182822d6817184a5bb596ed4d70c6949d9da7cd4d"
},
"downloads": -1,
"filename": "CodonU-1.0.2.tar.gz",
"has_sig": false,
"md5_digest": "07f1a816b3335d8c1b8c9ea88ceefe0d",
"packagetype": "sdist",
"python_version": "source",
"requires_python": null,
"size": 21581,
"upload_time": "2023-04-24T07:20:20",
"upload_time_iso_8601": "2023-04-24T07:20:20.915507Z",
"url": "https://files.pythonhosted.org/packages/18/23/e28f322c06ce1794ed29acc087ef810e45b10185f5102838fbbc91399c1a/CodonU-1.0.2.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2023-04-24 07:20:20",
"github": true,
"gitlab": false,
"bitbucket": false,
"github_user": "SouradiptoC",
"github_project": "codon_usage",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [],
"lcname": "codonu"
}
JSON
