SingleR | Bioconductor repository for the SingleR package | Genomics library

SingleR is a R library typically used in Artificial Intelligence, Genomics applications. SingleR has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Recent advances in single cell RNA-seq (scRNA-seq) have enabled an unprecedented level of granularity in characterizing gene expression changes in disease models. Multiple single cell analysis methodologies have been developed to detect gene expression changes and to cluster cells by similarity of gene expression. However, the classification of clusters by cell type relies heavily on known marker genes, and the annotation of clusters is performed manually. This strategy suffers from subjectivity and limits adequate differentiation of closely related cell subsets. Here, we present SingleR, a novel computational method for unbiased cell type recognition of scRNA-seq. SingleR leverages reference transcriptomic datasets of pure cell types to infer the cell of origin of each of the single cells independently. For more informations please refer to the manuscript: Aran, Looney, Liu et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nature Immunology (2019). This repository contains a simplified, more performant version of SingleR. The original repository containing the legacy version can be found here. This version does not support the browser application that accompanied the original version.