PIVOT: platform for interactive analysis and visualization of transcriptomics data

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Primary Cell Culture of Live Neurosurgically Resected Aged Adult Human Brain Cells and Single Cell Transcriptomics

(2017) Jennifer M. Spaethling et al.   Cell Reports

A predictive computational framework for direct reprogramming between human cell types

(2016) Owen J L Rackham et al.   NATURE GENETICS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

A survey of human brain transcriptome diversity at the single cell level

(2015) Spyros Darmanis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation

(2015) Hannah Dueck et al.   GENOME BIOLOGY

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

RNASeqGUI: a GUI for analysing RNA-Seq data

(2014) Francesco Russo et al.   BIOINFORMATICS

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

(2014) S. Anders et al.   BIOINFORMATICS

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

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

(2014) Peng Cui et al.   GENOME BIOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis

(2012) M.-A. Dillies et al.   BRIEFINGS IN BIOINFORMATICS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Penalized classification using Fisher's linear discriminant

(2011) Daniela M. Witten et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Whole-exome sequencing for finding de novo mutations in sporadic mental retardation

(2011) Peter N Robinson   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS