TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool.

Area of Science:

• Oncology
• Bioinformatics
• Genomics

Background:

• The tumor microenvironment (TME) comprises diverse cells, including stromal fibroblasts, immune cells, and malignant cells.
• Single-cell RNA sequencing (scRNA-seq) is crucial for elucidating TME composition.
• Existing scRNA-seq data for TME is fragmented across various cancer types, lacking a centralized repository.

Purpose of the Study:

• To establish a comprehensive database for TME scRNA-seq data.
• To develop an accessible tool, TMExplorer (an R package), for investigating the TME.
• To streamline the analysis and integration of TME scRNA-seq data into existing research pipelines.

Main Methods:

• Construction of a dedicated database to aggregate TME scRNA-seq datasets.
• Development of the TMExplorer R package providing a user-friendly interface.
• Implementation of robust search functionalities for dataset retrieval based on metadata and characteristics.

Main Results:

• A centralized database of TME scRNA-seq data has been successfully created.
• The TMExplorer R package offers easy access to datasets and metadata.
• Users can efficiently search and analyze TME composition using scRNA-seq data through the TMExplorer interface.

Conclusions:

• TMExplorer provides a valuable resource for cancer researchers studying the TME.
• The package facilitates a streamlined approach to TME analysis using scRNA-seq data.
• This resource promotes easier integration and broader accessibility of TME-related single-cell data.