scTransSort: Transformers for Intelligent Annotation of Cell Types by Gene Embeddings

Transformers in Vision: A Survey

(2022) Salman Khan et al.   ACM COMPUTING SURVEYS

ACTIVA: realistic single-cell RNA-seq generation with automatic cell-type identification using introspective variational autoencoders

(2022) A Ali Heydari et al.   BIOINFORMATICS

Single-cell Iso-Sequencing enables rapid genome annotation for scRNAseq analysis

(2022) Hope M Healey et al.   GENETICS

Intelligent fault diagnosis and visual interpretability of rotating machinery based on residual neural network

(2022) Shihang Yu et al.   MEASUREMENT

TDMSAE: A transferable decoupling multi-scale autoencoder for mechanical fault diagnosis

(2022) Shihang Yu et al.   MECHANICAL SYSTEMS AND SIGNAL PROCESSING

Automated methods for cell type annotation on scRNA-seq data

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

Evaluation of machine learning approaches for cell-type identification from single-cell transcriptomics data

(2021) Yixuan Huang et al.   BRIEFINGS IN BIOINFORMATICS

scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network

(2021) Xin Shao et al.   NUCLEIC ACIDS RESEARCH

From bulk, single-cell to spatial RNA sequencing

(2021) Xinmin Li et al.   International Journal of Oral Science

Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration

(2021) David W. McKellar et al.   Communications Biology

New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data

(2020) Xin Shao et al.   Protein & Cell

FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman–Rafsky non-parametric test

(2020) Yun Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Single-Cell Transcriptome Analysis in Plants: Advances and Challenges

(2020) Rahul Shaw et al.   Molecular Plant

Phenotypically supervised single-cell sequencing parses within-cell-type heterogeneity

(2020) Kevin Chen et al.   iScience

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

ACTINN: Automated Identification of Cell Types in Single Cell RNA Sequencing

(2019) Feiyang Ma et al.   BIOINFORMATICS

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

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

SCINA: Semi-Supervised Analysis of Single Cells in Silico

(2019) Zhang et al.   Genes

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

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

(2019) Allen W. Zhang et al.   NATURE METHODS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Identifying cell populations with scRNASeq

(2018) Tallulah S. Andrews et al.   MOLECULAR ASPECTS OF MEDICINE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Cell type transcriptome atlas for the planarianSchmidtea mediterranea

(2018) Christopher T. Fincher et al.   SCIENCE

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

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

(2018) et al.   NATURE

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning

(2017) Bo Wang et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS