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The Lair: a resource for exploratory analysis of published RNA-Seq data

Pimentel, Harold and Sturmfels, Pascal and Bray, Nicolas and Melsted, Páll and Pachter, Lior (2016) The Lair: a resource for exploratory analysis of published RNA-Seq data. BMC Bioinformatics, 17 (1). Art. No. 490. ISSN 1471-2105. PMCID PMC5131447. doi:10.1186/s12859-016-1357-2. https://resolver.caltech.edu/CaltechAUTHORS:20190506-141348569

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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


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1186/s12859-016-1357-2DOIArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131447PubMed CentralArticle
ORCID:
AuthorORCID
Melsted, Páll0000-0002-8418-6724
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2016 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Received: 3 June 2016; Accepted: 19 November 2016; Published: 1 December 2016. We thank the members of the Pachter Lab for contributing design and feature ideas and for suggesting the initial datasets with which to prototype The Lair. We thank the reviewers for testing our software and providing helpful comments and suggestions. HP and LP were partially supported by NIH grants R01 HG006129, R01 DK094699 and R01 HG008164. Availability of data and materials: The main user website and database is at http://pachterlab.github.io/lair. The workflow software is at https://github.com/pachterlab/bears_analyses and the website code is at http://pachterlab.github.io/lair. Access to all webpages is free of charge. All software is released under GPLv3. Authors’ contributions: HP, NB, PM and LP conceived the idea. HP and PS developed The Lair system. HP, PS and LP analyzed data. HP and LP wrote the manuscript. All authors read and approved the final manuscript. Authors’ information: Not applicable. The authors declare that they have no competing interests. Consent for publication: Not applicable. Ethics approval and consent to participate: Not applicable.
Funders:
Funding AgencyGrant Number
NIHR01 HG006129
NIHR01 DK094699
NIHR01 HG008164
Subject Keywords:RNA-Seq, Sequence read archive, Exploratory data analysis, Shiny, Interactive visualization, Reanalysis, Reproducibility, Kallisto, Sleuth
Issue or Number:1
PubMed Central ID:PMC5131447
DOI:10.1186/s12859-016-1357-2
Record Number:CaltechAUTHORS:20190506-141348569
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190506-141348569
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:95256
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:06 May 2019 21:29
Last Modified:16 Nov 2021 17:11

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