ljw-struggle / pymmdb

single-cell multimodal omics database

python API package of single-cell multimodal omics database (pymmdb)

Introduction

pymmdb is a python package that provides the interface to access the datasets in scMMDB.

Installation

Install from PyPI

$ pip install pymmdb

Install from Source

# 1.Clone the source code from github
$ git clone https://github.com/ljw-struggle/pymmdb.git
$ cd pymmdb
    
# 2. Create a conda environment and activate it.
$ conda env create -n pymmdb --file env.yml
$ conda activate pymmdb

# 3. Install pymmdb as a dependency or third-party package with pip.
$ python setup.py install # or python setup.py develop or pip install -e .

Usage

import pymmdb
mmdb = pymmdb.MMDB() # Create a MMDB object
dataset = mmdb.load_dataset('Dataset_A_000') # Load a specific dataset

Please refer to 📘Documentation and Tutorials for more details.

Cite

Jiawei Li, Mengyuan Zhao, Jiahui Yan, Yanlin Jiang, Zongbo Han, Shizhan Chen, Wei Li, Limin Jiang, Louxin Zhang, Fang Wang, Jijun Tang, Fei Guo. scMMDB: a comprehensive resource and knowledgebase for multimodal omics data at the single-cell resolution, 2024