title: The Lair: a resource for exploratory analysis of published RNA-Seq data.
abstract: Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is difficult to use in practice. We introduce a series of tools for processing and analyzing RNA-Seq data in the Sequence Read Archive, that together have allowed us to build an easily extendable resource for analysis of data underlying published papers. Our system makes the exploration of data easily accessible and usable without technical expertise. Our database and associated tools can be accessed at The Lair: http://pachterlab.github.io/lair .
authors.affiliation: Department of Computer Science, University of California, Berkeley, 387 Soda Hall, Berkeley, 94720, USA.
authors.forename: Harold
authors.initials: H
authors.lastname: Pimentel
authors.affiliation: Department of Computer Science, University of Michigan, 486 Vassar Avenue, Berkeley, CA, 94708, USA.
authors.forename: Pascal
authors.initials: P
authors.lastname: Sturmfels
authors.affiliation: Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA, 94720, USA.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bray
authors.affiliation: Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Dunhagi 5, 107, Reykjavík, Iceland.
authors.forename: Páll
authors.initials: P
authors.lastname: Melsted
authors.affiliation: Department of Computer Science, University of California, Berkeley, 387 Soda Hall, Berkeley, 94720, USA. lpachter@math.berkeley.edu.|Departments of Mathematics and Molecular & Cell Biology, University of California at Berkeley, Berkeley, CA, 94720-3840, USA. lpachter@math.berkeley.edu.
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
mesh_terms: D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
keywords: Exploratory data analysis; Interactive visualization; Kallisto; RNA-Seq; Reanalysis; Reproducibility; Sequence read archive; Shiny; Sleuth