IRIS-EDA: An integrated RNA-Seq interpretation system for gene expression data analysis

Data visualization tools drive interactivity and reproducibility in online publishing

(2018) Jeffrey M. Perkel   NATURE

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

A comprehensive evaluation of module detection methods for gene expression data

(2018) Wouter Saelens et al.   Nature Communications

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

(2017) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

VisRseq: R-based visual framework for analysis of sequencing data

(2015) Hamid Younesy et al.   BMC BIOINFORMATICS

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

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

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor

(2012) Xun Xu et al.   CELL

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

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

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

QUBIC: a qualitative biclustering algorithm for analyses of gene expression data

(2009) Guojun Li et al.   NUCLEIC ACIDS RESEARCH

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS