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

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...

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Veröffentlicht in:PloS one 2022-09, Vol.17 (9), p.e0272302
Hauptverfasser: Christensen, Erik, Naidas, Alaine, Chen, David, Husic, Mia, Shooshtari, Parisa
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Sprache:eng
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Zusammenfassung: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. 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
1932-6203
DOI:10.1371/journal.pone.0272302