Benchmarking single cell RNA-sequencing analysis pipelines using mixture control experiments

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

(2019) Michael B. Cole et al.   Cell Systems

DrImpute: imputing dropout events in single cell RNA sequencing data

(2018) Wuming Gong et al.   BMC BIOINFORMATICS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data

(2018) Shun H Yip et al.   BRIEFINGS IN BIOINFORMATICS

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

SAVER: gene expression recovery for single-cell RNA sequencing

(2018) Mo Huang et al.   NATURE METHODS

Bias, robustness and scalability in single-cell differential expression analysis

(2018) Charlotte Soneson et al.   NATURE METHODS

FateID infers cell fate bias in multipotent progenitors from single-cell RNA-seq data

(2018) Josip S Herman et al.   NATURE METHODS

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data

(2018) Luyi Tian et al.   PLoS Computational Biology

A test metric for assessing single-cell RNA-seq batch correction

(2018) Maren Büttner et al.   NATURE METHODS

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

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

(2017) Huipeng Li et al.   NATURE GENETICS

SCnorm: robust normalization of single-cell RNA-seq data

(2017) Rhonda Bacher et al.   NATURE METHODS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Linnorm: improved statistical analysis for single cell RNA-seq expression data

(2017) Shun H. Yip et al.   NUCLEIC ACIDS RESEARCH

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Batch effects and the effective design of single-cell gene expression studies

(2017) Po-Yuan Tung et al.   Scientific Reports

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

RNA-seq mixology: designing realistic control experiments to compare protocols and analysis methods

(2016) Aliaksei Z. Holik et al.   NUCLEIC ACIDS RESEARCH

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

A Single-Cell Transcriptome Atlas of the Human Pancreas

(2016) Mauro J. Muraro et al.   Cell Systems

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

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

(2015) Catalina A. Vallejos et al.   PLoS Computational Biology

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS