scAnno: a deconvolution strategy-based automatic cell type annotation tool for single-cell RNA-sequencing data sets

A single-cell atlas of the multicellular ecosystem of primary and metastatic hepatocellular carcinoma

(2022) Yiming Lu et al.   Nature Communications

Automated methods for cell type annotation on scRNA-seq data

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

Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics

(2021) Christoph Muus et al.   NATURE MEDICINE

Critical downstream analysis steps for single-cell RNA sequencing data

(2021) Zilong Zhang et al.   BRIEFINGS IN BIOINFORMATICS

scMAGIC: accurately annotating single cells using two rounds of reference-based classification

(2021) Yu Zhang et al.   NUCLEIC ACIDS RESEARCH

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

SciBet as a portable and fast single cell type identifier

(2020) Chenwei Li et al.   Nature Communications

Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma

(2020) Yu-Pei Chen et al.   CELL RESEARCH

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference

(2020) Yingxin Lin et al.   Molecular Systems Biology

A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples

(2020) Huamei Li et al.   BMC GENOMICS

Single-cell landscape of the ecosystem in early-relapse hepatocellular carcinoma

(2020) Yunfan Sun et al.   CELL

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles

(2019) Peng Xie et al.   NUCLEIC ACIDS RESEARCH

scMatch: a single-cell gene expression profile annotation tool using reference datasets

(2019) Rui Hou et al.   BIOINFORMATICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

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

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

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

(2019) P. Ramachandran et al.   NATURE

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

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

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

(2018) Sonya A. MacParland et al.   Nature Communications

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain

(2016) B. B. Lake et al.   SCIENCE

Differences and similarities between human and chimpanzee neural progenitors during cerebral cortex development

(2016) Felipe Mora-Bermúdez et al.   eLife

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

(2015) J. Gray Camp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

An expression atlas of human primary cells: inference of gene function from coexpression networks

(2013) Neil A Mabbott et al.   BMC GENOMICS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY