Augusta
==========
Python package: From RNA-Seq to the Boolean Network through the Gene Regulatory Network
Documentation and tutorials are available at `augusta.readthedocs.io <https://augusta.readthedocs.io>`_.
Quick Guide
----------------
Dependencies:
- Python 3, versions 3.7 and 3.8
- Docker
**Installation:**
We highly recomment installing and using Augusta in a virtual environment.
.. code-block::
$ conda create -n Augusta_venv python=3.7 anaconda
$ conda activate Augusta_venv
.. code-block::
$ pip install Augusta
**Usage:**
See `Inputs <https://augusta.readthedocs.io/en/latest/User%20guide.html>`_ for details about input files and variables.
.. code-block::
$ python
>>> import Augusta
GRN and BN inference using RNA-Seq:
.. code-block::
>>> Augusta.RNASeq_to_BN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string', motifs_max_time = My_seconds)
GRN inference using RNA-Seq:
.. code-block::
>>> Augusta.RNASeq_to_GRN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string', motifs_max_time = My_seconds)
BN inference using GRN:
.. code-block::
>>> Augusta.GRN_to_BN(GRN_input = 'MyGRN_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', add_dbs_info = 'My_string')
GRN refinement:
.. code-block::
>>> Augusta.refineGRN(GRN_input = 'MyGRN_file.csv', genbank_file_input = 'MyGB_file.gb', count_table_input = 'MyCT_file.csv', promoter_length = My_number, motifs_max_time = My_seconds)
Raw data
{
"_id": null,
"home_page": "https://github.com/JanaMus/Augusta",
"name": "Augusta",
"maintainer": "",
"docs_url": null,
"requires_python": ">=3.7, <3.9",
"maintainer_email": "",
"keywords": "Computational biology,Bioinformatics,RNA-Seq,mutual information,database,Boolean network,Gene Regulatory network,SBML",
"author": "Jana Musilova, Zdenek Vafek, Karel Sedlar",
"author_email": "musilovajana@vut.cz",
"download_url": "https://files.pythonhosted.org/packages/c2/7e/6f7aa63ea9d130a4ad7e8ba79453cb96b33b7ab2f46c97059dd6036f30f7/Augusta-1.0.5.tar.gz",
"platform": null,
"description": "Augusta\n==========\n\nPython package: From RNA-Seq to the Boolean Network through the Gene Regulatory Network\n\nDocumentation and tutorials are available at `augusta.readthedocs.io <https://augusta.readthedocs.io>`_.\n\nQuick Guide\n----------------\n\nDependencies:\n\n- Python 3, versions 3.7 and 3.8\n- Docker\n\n**Installation:**\n\nWe highly recomment installing and using Augusta in a virtual environment.\n\n.. code-block::\n\n $ conda create -n Augusta_venv python=3.7 anaconda\n $ conda activate Augusta_venv\n \n\n.. code-block::\n\n $ pip install Augusta\n\n\n**Usage:** \n\nSee `Inputs <https://augusta.readthedocs.io/en/latest/User%20guide.html>`_ for details about input files and variables.\n\n.. code-block:: \n\n $ python\n >>> import Augusta\n \nGRN and BN inference using RNA-Seq:\n\n.. code-block:: \n\n >>> Augusta.RNASeq_to_BN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string', motifs_max_time = My_seconds)\n\nGRN inference using RNA-Seq:\n\n.. code-block:: \n\n >>> Augusta.RNASeq_to_GRN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string', motifs_max_time = My_seconds)\n\n\nBN inference using GRN:\n\n.. code-block:: \n\n >>> Augusta.GRN_to_BN(GRN_input = 'MyGRN_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', add_dbs_info = 'My_string')\n\n\nGRN refinement:\n\n.. code-block:: \n\n >>> Augusta.refineGRN(GRN_input = 'MyGRN_file.csv', genbank_file_input = 'MyGB_file.gb', count_table_input = 'MyCT_file.csv', promoter_length = My_number, motifs_max_time = My_seconds)\n \n\n\n\n",
"bugtrack_url": null,
"license": "MIT",
"summary": "Python package for inference of the gene regulatory network and the boolean network using RNA-Seq data.",
"version": "1.0.5",
"project_urls": {
"Homepage": "https://github.com/JanaMus/Augusta"
},
"split_keywords": [
"computational biology",
"bioinformatics",
"rna-seq",
"mutual information",
"database",
"boolean network",
"gene regulatory network",
"sbml"
],
"urls": [
{
"comment_text": "",
"digests": {
"blake2b_256": "6a021da3283a7de45c2cd9fe9fc28167572156b5e6c5fd7a9d5be99dcaf046cd",
"md5": "0ad353e4622a79ec8ed67c593a71f779",
"sha256": "664f488b0134eee0329b80ecb13e3339008c7816b5e98f4d1680211b09e6fbe7"
},
"downloads": -1,
"filename": "Augusta-1.0.5-py3-none-any.whl",
"has_sig": false,
"md5_digest": "0ad353e4622a79ec8ed67c593a71f779",
"packagetype": "bdist_wheel",
"python_version": "py3",
"requires_python": ">=3.7, <3.9",
"size": 140058,
"upload_time": "2024-01-22T13:48:46",
"upload_time_iso_8601": "2024-01-22T13:48:46.558207Z",
"url": "https://files.pythonhosted.org/packages/6a/02/1da3283a7de45c2cd9fe9fc28167572156b5e6c5fd7a9d5be99dcaf046cd/Augusta-1.0.5-py3-none-any.whl",
"yanked": false,
"yanked_reason": null
},
{
"comment_text": "",
"digests": {
"blake2b_256": "c27e6f7aa63ea9d130a4ad7e8ba79453cb96b33b7ab2f46c97059dd6036f30f7",
"md5": "036e83d2031c877c4b8be66162e10720",
"sha256": "3c16a179bed9eda7d152c5455b027cf769f53047bb22284e80e5c0665eb79645"
},
"downloads": -1,
"filename": "Augusta-1.0.5.tar.gz",
"has_sig": false,
"md5_digest": "036e83d2031c877c4b8be66162e10720",
"packagetype": "sdist",
"python_version": "source",
"requires_python": ">=3.7, <3.9",
"size": 120731,
"upload_time": "2024-01-22T13:48:48",
"upload_time_iso_8601": "2024-01-22T13:48:48.647452Z",
"url": "https://files.pythonhosted.org/packages/c2/7e/6f7aa63ea9d130a4ad7e8ba79453cb96b33b7ab2f46c97059dd6036f30f7/Augusta-1.0.5.tar.gz",
"yanked": false,
"yanked_reason": null
}
],
"upload_time": "2024-01-22 13:48:48",
"github": true,
"gitlab": false,
"bitbucket": false,
"codeberg": false,
"github_user": "JanaMus",
"github_project": "Augusta",
"travis_ci": false,
"coveralls": false,
"github_actions": true,
"requirements": [
{
"name": "pandas",
"specs": []
},
{
"name": "numpy",
"specs": []
},
{
"name": "scikit-learn",
"specs": []
},
{
"name": "bioinfokit",
"specs": []
},
{
"name": "Bio",
"specs": []
},
{
"name": "docker",
"specs": []
},
{
"name": "EcoNameTranslator",
"specs": []
},
{
"name": "mygene",
"specs": []
},
{
"name": "omnipath",
"specs": []
},
{
"name": "urllib3",
"specs": [
[
">=",
"1.26.0"
]
]
},
{
"name": "requests",
"specs": [
[
">=",
"2.24.0"
]
]
},
{
"name": "bs4",
"specs": []
},
{
"name": "lxml",
"specs": []
},
{
"name": "html5lib",
"specs": []
},
{
"name": "networkx",
"specs": [
[
"==",
"1.11"
]
]
},
{
"name": "easydev",
"specs": []
},
{
"name": "colormap",
"specs": []
},
{
"name": "ccapi",
"specs": [
[
"==",
"0.1.0"
]
]
}
],
"lcname": "augusta"
}
JSON
