scEMAIL: Universal and Source-free Annotation Method for scRNA-seq Data with Novel Cell-type Perception

scNAME: neighborhood contrastive clustering with ancillary mask estimation for scRNA-seq data

(2022) Hui Wan et al.   BIOINFORMATICS

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

(2021) Chenling Xu et al.   Molecular Systems Biology

Mapping single-cell data to reference atlases by transfer learning

(2021) Mohammad Lotfollahi et al.   NATURE BIOTECHNOLOGY

Benchmarking atlas-level data integration in single-cell genomics

(2021) Malte D. Luecken et al.   NATURE METHODS

Tools for the analysis of high-dimensional single-cell RNA sequencing data

(2020) Yan Wu et al.   Nature Reviews Nephrology

Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST

(2020) Zhi-Jie Cao et al.   Nature Communications

Single-cell RNA-seq data semi-supervised clustering and annotation via structural regularized domain adaptation

(2020) Liang Chen et al.   BIOINFORMATICS

Conditional out-of-distribution generation for unpaired data using transfer VAE

(2020) Mohammad Lotfollahi et al.   BIOINFORMATICS

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

(2019) Jurrian K de Kanter et al.   NUCLEIC ACIDS RESEARCH

SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

(2019) Yuqi Tan et al.   Cell Systems

Supervised classification enables rapid annotation of cell atlases

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

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

The adult human testis transcriptional cell atlas

(2018) Jingtao Guo et al.   CELL RESEARCH

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing

(2017) Karsten Bach et al.   Nature Communications

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS