Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Single-Cell Transcriptomics Bioinformatics and Computational Challenges

(2016) Olivier B. Poirion et al.   Frontiers in Genetics

Sincell: an R/Bioconductor package for statistical assessment of cell-state hierarchies from single-cell RNA-seq: Fig. 1.

(2015) Miguel Juliá et al.   BIOINFORMATICS

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells

(2015) Kyu-Tae Kim et al.   GENOME BIOLOGY

Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos

(2015) Xiaoying Fan et al.   GENOME BIOLOGY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing

(2013) Zhigang Xue et al.   NATURE

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

A flexible R package for nonnegative matrix factorization

(2010) Renaud Gaujoux et al.   BMC BIOINFORMATICS

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

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

PPAR-γAgonists and Their Effects on IGF-I Receptor Signaling: Implications for Cancer

(2009) A. Belfiore et al.   PPAR Research

NVP-AUY922: A Novel Heat Shock Protein 90 Inhibitor Active against Xenograft Tumor Growth, Angiogenesis, and Metastasis

(2008) S. A. Eccles et al.   CANCER RESEARCH