Article ; Online: Exploring and analysing single cell multi-omics data with VDJView.
BMC medical genomics
2020 Volume 13, Issue 1, Page(s) 29
Abstract: Background: Single cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simultaneously analyse large multi- ... ...
| Abstract | Background: Single cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simultaneously analyse large multi-omics datasets integrated with metadata such as patient and clinical information. Results: We developed VDJView, which permits the simultaneous or independent analysis and visualisation of gene expression, immune receptors, and clinical metadata of both T and B cells. This tool is implemented as an easy-to-use R shiny web-application, which integrates numerous gene expression and TCR analysis tools, and accepts data from plate-based sorted or high-throughput single cell platforms. We utilised VDJView to analyse several 10X scRNA-seq datasets, including a recent dataset of 150,000 CD8 Conclusions: VDJView enables researchers without profound bioinformatics skills to analyse immune scRNA-seq data, integrating and visualising this with clonality and metadata profiles, thus accelerating the process of hypothesis testing, data interpretation and discovery of cellular heterogeneity. VDJView is freely available at https://bitbucket.org/kirbyvisp/vdjview. |
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| MeSH term(s) | B-Lymphocytes/immunology ; B-Lymphocytes/pathology ; Breast Neoplasms/genetics ; Breast Neoplasms/immunology ; Breast Neoplasms/pathology ; CD8-Positive T-Lymphocytes/immunology ; CD8-Positive T-Lymphocytes/pathology ; Databases, Nucleic Acid ; Female ; Gene Expression Regulation, Neoplastic/immunology ; Humans ; RNA-Seq ; Single-Cell Analysis ; Software |
| Language | English |
| Publishing date | 2020-02-18 |
| Publishing country | England |
| Document type | Journal Article ; Research Support, Non-U.S. Gov't |
| ISSN | 1755-8794 |
| ISSN (online) | 1755-8794 |
| DOI | 10.1186/s12920-020-0696-z |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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