Single-Cell Multimodal Omics DataBase (scMMDB) is a comprehensive repository for general paired single-cell multimodal omics data, encompassing both epigenomics, transcriptomics and proteomics data, and provides dataset/element search, visualization and download with unified formats.

API Usage

pymmdb
To facilitate integration and reuse within relevant python tools, we have provided pymmdb that enables users to query, download, or directly load one specific dataset of interest within python environment.

Manual

Browsing Dataset
The dataset search page contains a list of all the datasets incorporated in scMMDB. The important information of datasets such as Species, Tissues and Technology are visualized in columns and are searchable. Users can browse all the datasets within the list and search interested datasets with specific information.
(1) Select "Data" to enter this page.
(2) Filter datasets by specific information.
(3) Choose one dataset of interest to explore.
Exploring Dataset
The dataset exploration page contains five modules to help users to explore data in detail.
(1) Show some important information of the dataset and provide the download link of the preprocessed file.
(2) Explore the cell metadata and single-cell omics data in the single-omics view.
(3) Explore the cell metadata and single-cell omics data in the multi-omics view.
(4) Show some statistic plots of the dataset.
(The visualization module of data exploration page can give users intuitive understanding of the dataset.)
Search Element
The element search page contains the search function of elements (promoter, gene, protein) contained in scMMDB.
(1) Select “Search” to enter this page.
(2) Search element by element name.
(3) Search information of the element.
Exploring Element
The page of element exploration page contains two modules to help users to explore element in detail.
(1) Show some summary information of the element (promoter, gene, protein).
(2) List the corresponding datasets which detect the element in single cell level. Users can browse these datasets and chose one to explore.
(3) The Datasets tab in the page of one searched protein provides two data comparison functions. Users can choose two interested proteins from the data list to compare. (Choose "Compare Expression" to compare element expression distribution between two datasets. Choose "Compare Correlation" to compare element correlation patters between two datasets.)
Limitations
The limitations of the current version of scMMDB.
(1) The current version of MMDB only focus on the Epgenomics, Transcriptomics and Proteomics.
(2) The current version of MMDB haven't collected spatial single-cell multi-omics data.

scMMDB is developed by TJU, CSU, SIAT and HIT. For help, please refer to the manual link in the navigation bar, or contact us via ljwstruggle@gmail.com (Jiawei Li).

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