GEfetch2R

GEfetch2R is designed to accelerate users’ downloading and preparation of single-cell/bulk RNA-seq datasets from public resources. GEfetch2R supports downloading various scRNA-seq data types, including raw data (SRA and ENA), count matrix (GEO, UCSC Cell Browser, and PanglaoDB), and processed object (GEO, Zenodo, CELLxGENE, and HCA); can access and explore existing scRNA-seq data, load output/downloaded count matrices and annotations to R (SeuratObject/DESeqDataSet), extract a subset of the SeuratObject based on cell metadata and genes, and merge multiple SeuratObjects if applicable; provides format conversions between different scRNA-seq objects, including SeuratObject, AnnData, SingleCellExperiment, CellDataSet/cell_data_set, and loom.