Codeplot
singleR
Introduction

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 only has to be done once, for the reference dataset, and this biological knowledge can be propagated to new datasets in an automated manner.

Script
Input
Task nameAttribute nameTypeDescription
* run_singler.singler refString Reference dataset recommended by singleR.such as HumanPrimaryCellAtlasData,BlueprintEncodeData,ImmGenData,DatabaseImmuneCellExpressionData,NovershternHematopoieticData,MouseRNAseqData,MonacoImmuneData
* run_singler.singler input_fileFile Input matrix file to be annotated, support h5AD, TSV. CSV, RDS format
* run_singler.singler custom_refFile custom datatset,RDS format
Output
Task nameAttribute nameTypeDescription
* run_singler heatmapFile output heatmap figure
* run_singler resultFile output csv
* run_singler distriFile output delta distribution figure