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...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2022-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0272302 |
| _version_ | 1828110842037534720 |
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| author | Erik Christensen Alaine Naidas David Chen Mia Husic Parisa Shooshtari |
| author_facet | Erik Christensen Alaine Naidas David Chen Mia Husic Parisa Shooshtari |
| author_sort | Erik Christensen |
| collection | DOAJ |
| description | <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. |
| first_indexed | 2024-04-11T11:24:31Z |
| format | Article |
| id | doaj.art-11bca2e5aa5f4200b51a474a891b5c69 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-11T11:24:31Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-11bca2e5aa5f4200b51a474a891b5c692022-12-22T04:26:19ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-01179e027230210.1371/journal.pone.0272302TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool.Erik ChristensenAlaine NaidasDavid ChenMia HusicParisa Shooshtari<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.https://doi.org/10.1371/journal.pone.0272302 |
| spellingShingle | Erik Christensen Alaine Naidas David Chen Mia Husic Parisa Shooshtari TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool. PLoS ONE |
| title | TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool. |
| title_full | TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool. |
| title_fullStr | TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool. |
| title_full_unstemmed | TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool. |
| title_short | TMExplorer: A tumour microenvironment single-cell RNAseq database and search tool. |
| title_sort | tmexplorer a tumour microenvironment single cell rnaseq database and search tool |
| url | https://doi.org/10.1371/journal.pone.0272302 |
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