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

Comparison of normalization and differential expression analyses using RNA-Seq data from 726 individual Drosophila melanogaster

(2016) Yanzhu Lin et al.   BMC GENOMICS

The contribution of cell cycle to heterogeneity in single-cell RNA-seq data

(2016) Andrew McDavid et al.   NATURE BIOTECHNOLOGY

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

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

(2015) Ning Leng et al.   NATURE METHODS

A cost-effective RNA sequencing protocol for large-scale gene expression studies

(2015) Zhonggang Hou et al.   Scientific Reports

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

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

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Cyclebase 3.0: a multi-organism database on cell-cycle regulation and phenotypes

(2014) Alberto Santos et al.   NUCLEIC ACIDS RESEARCH

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Chemically defined conditions for human iPSC derivation and culture

(2011) Guokai Chen et al.   NATURE METHODS

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL