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augusta

https://github.com/janamus/augusta

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (10.9%) to scientific vocabulary
Last synced: 7 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: JanaMus
  • License: mit
  • Language: Python
  • Default Branch: master
  • Size: 8.92 MB
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created over 3 years ago · Last pushed 11 months ago
Metadata Files
Readme License Citation

README.rst 

Augusta
==========

Python package: From RNA-Seq to the Boolean Network through the Gene Regulatory Network

Documentation and tutorials are available at `augusta.readthedocs.io `_.


News
----------------
Augusta is FAIR!

We are excited to announce that Augusta has undergone a successful FAIRification process. This process was part of the FAIR-IMPACT workshop, which aims to ensure that research software is Findable, Accessible, Interoperable, and Reusable (FAIR). You can read more about our FAIRification journey and how it enhances Augusta’s usability and collaboration potential in the FAIR-IMPACT Implementation Story: `FAIRification of Augusta, Research Software for Gene Regulatory Networks and Boolean Models Inference | FAIR-IMPACT `_.



Credits
----------------
The Augusta project is based on research detailed in the following paper. Please cite this paper when using or referencing our work:

Augusta: From RNA‐Seq to gene regulatory networks and Boolean models. Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomas Helikar, and Karel Sedlar. *Computational and Structural Biotechnology Journal*, 2024. DOI: `10.1016/j.csbj.2024.01.013 `_.


Contributors
----------------
- Jana Musilova, musilovaj22@gmail.com
- Zdenek Vafek
- Karel Sedlar, sedlar@vut.cz



Quick Guide
----------------

Dependencies:

- Python: version 3.7 or 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 `_ 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)

Owner

  • Name: Jana Musilova
  • Login: JanaMus
  • Kind: user

Citation (CITATION.cff) 

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Augusta
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Jana
    family-names: Musilova
    email: musilovaj22@gmail.com
    orcid: 'https://orcid.org/0000-0001-6910-6047'
    role: contributor
  - given-names: Zdenek
    family-names: Vafek
    role: contributor
  - given-names: Karel
    family-names: Sedlar
    orcid: 'https://orcid.org/0000-0002-8269-4020'
    role: contributor
repository-code: 'https://github.com/JanaMus/Augusta'
repository: 'https://augusta.readthedocs.io'
abstract: >-
  Python package: From RNA-Seq to the Boolean Network
  through the Gene Regulatory Network.
keywords:
  - biological network
  - Python
  - package
  - GRN
  - BN
  - RNA-Seq
license: MIT
identifiers:
  - type: doi
    value: 10.1016/j.csbj.2024.01.013

GitHub Events

Total
  • Create event: 1
  • Release event: 2
  • Issues event: 4
  • Push event: 13
Last Year
  • Create event: 1
  • Release event: 2
  • Issues event: 4
  • Push event: 13

Committers

Last synced: about 3 years ago

All Time
  • Total Commits: 126
  • Total Committers: 3
  • Avg Commits per committer: 42.0
  • Development Distribution Score (DDS): 0.063
Top Committers
Name Email Commits
Jana Musilova 5****s@u****m 118
Jana Musilová m****a@f****z 7
karelsedlar s****r@v****z 1
Committer Domains (Top 20 + Academic)
vut.cz: 1 feec.vutbr.cz: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 2
  • Total pull requests: 1
  • Average time to close issues: 23 days
  • Average time to close pull requests: 1 minute
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 0.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 0
  • Average time to close issues: 23 days
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 0
  • Average comments per issue: 0.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • JanaMus (1)
  • nickgladman (1)
Pull Request Authors
  • JanaMus (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 37 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 9
  • Total maintainers: 1
pypi.org: augusta

Python package for inference of the gene regulatory network and the boolean network using RNA-Seq data.

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 37 Last month
Rankings
Dependent packages count: 6.6%
Average: 26.7%
Forks count: 30.5%
Dependent repos count: 30.6%
Stargazers count: 39.1%
Maintainers (1)
JanaMus
Last synced: 7 months ago

Dependencies

requirements.txt pypi
  • Bio *
  • EcoNameTranslator *
  • bioinfokit *
  • bs4 *
  • ccapi ==0.1.0
  • docker *
  • html5lib *
  • lxml *
  • mygene *
  • networkx ==1.11
  • numpy *
  • omnipath *
  • pandas *
  • requests >=2.24.0
  • scikit-learn *