A comparison of single-cell trajectory inference methods

PROSSTT: probabilistic simulation of single-cell RNA-seq data for complex differentiation processes

(2019) Nikolaos Papadopoulos et al.   BIOINFORMATICS

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

(2018) Kelly Street et al.   BMC GENOMICS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

A comprehensive evaluation of module detection methods for gene expression data

(2018) Wouter Saelens et al.   Nature Communications

Exploring the single-cell RNA-seq analysis landscape with the scRNA-tools database

(2018) Luke Zappia et al.   PLoS Computational Biology

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Joint profiling of chromatin accessibility and gene expression in thousands of single cells

(2018) Junyue Cao et al.   SCIENCE

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

(2018) et al.   NATURE

ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

(2017) Marvin N. Wright et al.   Journal of Statistical Software

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Reproducibility of computational workflows is automated using continuous analysis

(2017) Brett K Beaulieu-Jones et al.   NATURE BIOTECHNOLOGY

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Mapping the human DC lineage through the integration of high-dimensional techniques

(2017) Peter See et al.   SCIENCE

Reconstructing cell cycle pseudo time-series via single-cell transcriptome data

(2017) Zehua Liu et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

SCOUP: a probabilistic model based on the Ornstein–Uhlenbeck process to analyze single-cell expression data during differentiation

(2016) Hirotaka Matsumoto et al.   BMC BIOINFORMATICS

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data

(2016) David A. duVerle et al.   BMC BIOINFORMATICS

Computational methods for trajectory inference from single-cell transcriptomics

(2016) Robrecht Cannoodt et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

Defining cell types and states with single-cell genomics

(2015) Cole Trapnell   GENOME RESEARCH

Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow

(2015) Andreas Schlitzer et al.   NATURE IMMUNOLOGY

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Quantitative Single-Cell Approaches to Stem Cell Research

(2014) Martin Etzrodt et al.   Cell Stem Cell

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Shape constrained additive models

(2014) Natalya Pya et al.   STATISTICS AND COMPUTING

OMICtools: an informative directory for multi-omic data analysis

(2014) V. J. Henry et al.   Database-The Journal of Biological Databases and Curation

Best Practices for Scientific Computing

(2014) Greg Wilson et al.   PLOS BIOLOGY

Temporal dynamics and transcriptional control using single-cell gene expression analysis

(2013) Tsukasa Kouno et al.   GENOME BIOLOGY

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

(2011) Thomas Schaffter et al.   BIOINFORMATICS

The self-assessment trap: can we all be better than average?

(2011) R. Norel et al.   Molecular Systems Biology