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13 de feb. de 2024 · Package ‘SingleR’ May 25, 2024 Title Reference-Based Single-Cell RNA-Seq Annotation Version 2.6.0 Date 2024-02-13 Description Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
13 de may. de 2024 · 6 SingleR. 6. SingleR. In this workshop we have focused on the Seurat package. However, there is another whole ecosystem of R packages for single cell analysis within Bioconductor. We won’t go into any detail on these packages in this workshop, but there is good material describing the object type online : OSCA.
DOI: 10.18129/B9.bioc.SingleR. Bioconductor version: Development (3.20) Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently. Author: Dvir Aran [aut, cph], Aaron Lun [ctb, cre], Daniel Bunis ...
SingleR is an automatic annotation method for single-cell RNA sequencing (scRNAseq) data (Aran et al. 2019) . Given a reference dataset of samples (single-cell or bulk) with known labels, it labels new cells from a test dataset based on similarity to the reference. Thus, the burden of manually interpreting clusters and defining marker genes ...
Det kræver, at man skal være god til at tage initiativ og planlægge. Det slipper du for som medlem i Minglr+. Her gør vi benarbejdet for dig. Vi inviterer andre singler og planlægger de gode oplevelser. Du skal blot tage beslutningen om at møde op. Når den beslutning er truffet, sørger vi for at det hele løber så nemt for dig som muligt.
SingleR() is made to be workflow/package agnostic - if you can get a matrix of normalized counts, you can use it. SingleCellExperiment objects can be used directly. Seurat objects can be converted to SingleCellExperiment objects via Seurat's as.SingleCellExperiment() function or their normalized counts can be retrieved via GetAssayData or ...
1.2 Method description. SingleR can be considered a robust variant of nearest-neighbors classification, with some tweaks to improve resolution for closely related labels. For each test cell: We compute the Spearman correlation between its expression profile and that of each reference sample. The use of Spearman’s correlation provides a ...
