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

ABSTRACT:

Motivation

The tumour microenvironment (TME) contains various cells including stromal fibroblasts, immune and malignant cells, and its composition can be elucidated using single-cell RNA sequencing (scRNA-seq). scRNA-seq datasets from several cancer types are available, yet we lack a comprehensive database to collect and present related TME data in an easily accessible format.

Results

We therefore built a TME scRNA-seq database, and created the R package TMExplorer to facilitate investigation of the TME. TMExplorer provides an interface to easily access all available datasets and their metadata. The users can search for datasets using a thorough range of characteristics. The TMExplorer allows for examination of the TME using scRNA-seq in a way that is streamlined and allows

SUBMITTER: Christensen E 

PROVIDER: S-EPMC9462821 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature