RNA sequencing analysis of the developing chicken retina

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Transcriptome profiling of developing photoreceptor subtypes reveals candidate genes involved in avian photoreceptor diversification

(2014) Jennifer M. Enright et al.   JOURNAL OF COMPARATIVE NEUROLOGY

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

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

(2013) Y. Liao et al.   BIOINFORMATICS

The Next-Generation Sequencing Revolution and Its Impact on Genomics

(2013) Daniel C. Koboldt et al.   CELL

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Rediscovering the chick embryo as a model to study retinal development

(2012) M Natalia Vergara et al.   Neural Development

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Analysis of retinal cell development in chick embryo by immunohistochemistry and in ovo electroporation techniques

(2010) Sung Doh et al.   BMC DEVELOPMENTAL 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