Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

Unbiased single-cell transcriptomic data cell type identification

Supervised cell type identification for scATAC-seq data

SCISSORS builds upon the Louvain graph-based clustering in Seurat by optimizing parameter selection when reclustering cell groups, with an eye towards identifying rare cell types.

The official implementation for "SANGO".

High precision, marker-based, hierarchical cell-type annotation tool for single-cell RNA-seq data

Unsupervised cell type identification for spatial transcriptomics

Hierarchical and high-resolution cell-type identification for single-cell RNA-seq data based on ScType.

Deep Learning single-cell Identification and Annotation

MarkerCount is a python3 cell-type identification toolkit for single-cell RNA-Seq experiments.

R package to assign an initial bone-related cell type