herbiv 0.1a2

HerbiV是一个具有多种功能的中药网络药理学分析工具，可进行经典的网络药理学及反向网络药理学分析。HerbiV is a multi-functional traditional chinese medicine network pharmacology analysis tool for classical network pharmacology and reverse network pharmacology.

HerbiV一个开发中的具有多种功能的中药网络药理学分析工具，可进行经典的网络药理学及反向网络药理学分析。

HerbiV is a multi-functional traditional chinese medicine network pharmacology analysis tool under development for classical network pharmacology and reverse network pharmacology.

• 中文

  • 安装
  • 使用
  • 更新日志

• English

  • Installation
  • Usage
  • Versions

中文

安装

可以使用pip安装HerbiV。

pip install herbiv

使用

基本使用

herbiv.analysis中提供了进行网络药理学分析的pipeline函数。

• reverse函数: 反向网络药理学分析的pipeline函数。使用它仅需使用命令

from herbiv import analysis
analysis.reverse(genes,
                 protein_chemical_links_path,
                 score,
                 save,
                 chemicals_path,
                 tcm_chemical_links_path,
                 tcm_path)

它需要一个必需形参genes，这是一个存储编码拟分析靶点的基因的Ensembl ID与其名称的字典，如{'9606.ENSP00000265022': 'DGKG'}。

它的可选形参有

• protein_chemical_links_path: 字符串类型，HerbiV_chemical_protein_links数据集的路径，默认为data/HerbiV_chemical_protein_links.csv；
• score: int类型，仅combined_score大于等于score的记录会被筛选出，默认为900；
• save: 布尔类型，是否保存原始分析结果，默认为True；
• chemicals_path: 字符串类型，HerbiV_chemicals数据集的路径，默认为data/HerbiV_chemicals.csv；
• tcm_chemical_links_path: 字符串类型，HerbiV_tcm_chemical_links数据集的路径，默认为data/HerbiV_tcm_chemical_links.csv；
• tcm_path: 字符串类型，HerbiV_tcm数据集的路径，默认为data/HerbiV_tcm.csv。

更新日志

0.0.1a1

• 横空出世

0.1a1(2323.3.28)

• 使用本项目自己的数据集进行分析，不再使用其他数据库的公共数据集，更新了整个分析架构，大大加快了分析速度；
• 加入了基于朴素贝叶斯的中药重要性评价模型。

English

HerbiV is a multi-functional traditional chinese medicine network pharmacology analysis tool for classical network pharmacology and reverse network pharmacology.

Installation

You can install HerbiV using pip.

pip install herbiv

Usage

Basic usage

herbiv.analysis provides pipeline function for network pharmacology analysis.

• reverse : pipeline function for reverse network pharmacology. To use it, please use command

from herbiv import analysis
analysis.reverse(genes,
                 protein_chemical_links_path,
                 score,
                 save,
                 chemicals_path,
                 tcm_chemical_links_path,
                 tcm_path)

It needs a required parameter genes, which is a dictionary that stores the Ensembl ID(s) of the gene(s) encoding the target(s) to be analyzed along with their name(s), e.g. {'9606.ENSP00000265022': 'DGKG'}.

Its optional parameter includes

• protein_chemical_links_path: str, path of the dataset HerbiV_chemical_protein_links, 9606.protein_chemical.links.transfer.v5.0.tsv by default;
• score: int, only when the combined_score is no less than it will be selected out, 900 by default;
• save: boolean，Whether to save the original analysis results, True by default;
• chemicals_path: str, path of the dataset HerbiV_chemicals, data/HerbiV_chemicals.csv by default;
• tcm_chemical_links_path: str, path of the dataset HerbiV_chemicals, data/HerbiV_chemicals.csv by default;
• tcm_path: str, path of the dataset HerbiV_tcm, data/HerbiV_tcm.csv by default.

Versions

0.0.1a1

• All start at here.

0.1a1(2323.3.28)

• Using the project's own datasets for analysis, instead of using public datasets from other databases. Updated the entire analysis architecture and greatly accelerated the analysis speed;
• Added a naive Bayes model-based importance evaluation model for TCM.