scGate: marker-based purification of cell types from heterogeneous single-cell RNA-seq datasets

Automated methods for cell type annotation on scRNA-seq data

(2021) Giovanni Pasquini et al.   Computational and Structural Biotechnology Journal

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data

(2020) Qianhui Huang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species

(2019) Rapolas Zilionis et al.   IMMUNITY

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

SCINA: Semi-Supervised Analysis of Single Cells in Silico

(2019) Zhang et al.   Genes

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL