TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool.
<h4>Motivation</h4>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 la...
| Hlavní autoři: | , , , , |
|---|---|
| Médium: | Článek |
| Jazyk: | English |
| Vydáno: |
Public Library of Science (PLoS)
2022-01-01
|
| Edice: | PLoS ONE |
| On-line přístup: | https://doi.org/10.1371/journal.pone.0272302 |
| Shrnutí: | <h4>Motivation</h4>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.<h4>Results</h4>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 for easy integration into already existing scRNA-seq analysis pipelines. |
|---|---|
| ISSN: | 1932-6203 |