BCseq: accurate single cell RNA-seq quantification with bias correction

Single-Cell Alternative Splicing Analysis with Expedition Reveals Splicing Dynamics during Neuron Differentiation

(2017) Yan Song et al.   MOLECULAR CELL

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

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

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

Beta-Poisson model for single-cell RNA-seq data analyses

(2016) Trung Nghia Vu et al.   BIOINFORMATICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Somatosensory neuron types identified by high-coverage single-cell RNA-sequencing and functional heterogeneity

(2015) Chang-Lin Li et al.   CELL RESEARCH

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

ROTS: reproducible RNA-seq biomarker detector—prognostic markers for clear cell renal cell cancer

(2015) Fatemeh Seyednasrollah et al.   NUCLEIC ACIDS RESEARCH

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

WemIQ: an accurate and robust isoform quantification method for RNA-seq data

(2014) Jing Zhang et al.   BIOINFORMATICS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A two-parameter generalized Poisson model to improve the analysis of RNA-seq data

(2010) Sudeep Srivastava et al.   NUCLEIC ACIDS RESEARCH

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

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

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