药理大师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。Pharmastar is a multi-functional traditional chinese medicine network pharmacology analysis tool for classical network pharmacology and reverse network pharmacology.
Project description
药理大师是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。
Pharmastar is a multi-functional traditional chinese medicine network pharmacology analysis tool under development for classical network pharmacology and reverse network pharmacology.
中文
使用
基本使用
pharmastar.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 pharmastar import analysis
analysis.reverse(genes,
protein_chemical_links_filename,
score,
chemicals_filename,
chunksize,
swiss_filename,
drug_likeness_num,
try_num)
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_filename
: 字符串类型,从STITCH数据库中下载的protein_chemical.links.transfer的文件名,默认为9606.protein_chemical.links.transfer.v5.0.tsv
;score
: int类型,仅combined_score大于等于score的记录会被筛选出,默认为900
;chemicals_filename
: 字符串类型,从STITCH数据库中下载的chemicals数据集的文件名,默认为chemicals.v5.0.tsv.gz
;param chunksize
: int类型,遍历chemicals数据集时的chunksize,该值过大可能耗尽计算机的内存,默认为1000000
;swiss_filename
: SwissADME的分析结果(csv文件)的路径,默认为swissadme.csv
;drug_likeness_num
: int类型,筛选类药性指标时至少有多少个为Yes,默认为3
;try_num
: int类型,pubchempy重复尝试的次数,默认为3
。
English
Pharmastar is a multi-functional traditional chinese medicine network pharmacology analysis tool for classical network pharmacology and reverse network pharmacology.
Usage
Basic usage
pharmastar.analysis
provides pipeline function for network pharmacology analysis.
reverse
: pipeline function for reverse network pharmacology. To use it, please use command
from pharmastar import analysis
analysis.reverse(genes,
protein_chemical_links_filename,
score,
chemicals_filename,
chunksize,
swiss_filename,
drug_likeness_num,
try_num)
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_filename
: dict, filename of the dataset protein_chemical.links.transfer from STITCH database,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;chemicals_filename
: str, filename of the dataset chemicals from STITCH database,chemicals.v5.0.tsv.gz
by default;param chunksize
: int, chunksize of the traversal to the chemicals dataset,the computer's memory may be exhausted if it is too large,1000000
by default;swiss_filename
: pathway of the SwissADME result,swissadme.csv
by default;drug_likeness_num
: int, how many 'Yes' at least when processing ADME selection,3
by default;try_num
: int, the number of times pubchempy tries,3
by default.
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