SCell: integrated analysis of single-cell RNA-seq data

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

(2014) Sean C. Bendall et al.   CELL

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Using Genome Query Language to uncover genetic variation

(2013) Christos Kozanitis et al.   BIOINFORMATICS

Normalization, bias correction, and peak calling for ChIP-seq

(2012) Aaron Diaz et al.   Statistical Applications in Genetics and Molecular Biology

A signal–noise model for significance analysis of ChIP-seq with negative control

(2010) Han Xu et al.   BIOINFORMATICS