Differential analysis of RNA-seq incorporating quantification uncertainty

Pimentel, Harold and Bray, Nicolas L. and Puente, Suzette and Melsted, Páll and Pachter, Lior (2017) Differential analysis of RNA-seq incorporating quantification uncertainty. Nature Methods, 14 (7). pp. 687-690. ISSN 1548-7091. doi:10.1038/nmeth.4324. https://resolver.caltech.edu/CaltechAUTHORS:20170612-084553487

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Abstract

We describe sleuth (http://pachterlab.github.io/sleuth), a method for the differential analysis of gene expression data that utilizes bootstrapping in conjunction with response error linear modeling to decouple biological variance from inferential variance. sleuth is implemented in an interactive shiny app that utilizes kallisto quantifications and bootstraps for fast and accurate analysis of data from RNA-seq experiments.

Item Type:

Article

Related URLs:

URL	URL Type	Description
http://dx.doi.org/10.1038/nmeth.4324	DOI	Article
http://rdcu.be/tpAk	Publisher	Free ReadCube access
http://biorxiv.org/content/early/2016/06/10/058164	Organization	Discussion Paper

ORCID:

Author	ORCID
Melsted, Páll	0000-0002-8418-6724
Pachter, Lior	0000-0002-9164-6231

Additional Information:

© 2017 Macmillan Publishers Limited, part of Springer Nature. Received 27 January 2017; Accepted 04 May 2017; Published online 05 June 2017. H.P. and L.P. were partially supported by NIH grant nos. R01 DK094699 and R01 HG006129. We thank D. Li, A. Tseng, and P. Sturmfels for help with implementing some of the interactive features in sleuth. Author Contributions: H.P. led the development of the sleuth statistical model and was assisted by S.P., N.L.B., P.M., and L.P. The method comparison and testing framework was designed by H.P., N.L.B., P.M., and L.P. The interactive sleuth live software was designed and implemented by H.P., as was the sleuth R package. H.P. automated production of the results. H.P., N.L.B., P.M., and L.P. analyzed results and wrote the paper. Data availability statement: The Bottomly data set is available at the NCBI Gene Expression Omnibus (GSE26024, accession nos. SRR099223–SRR099243). The Trapnell et al. data set (Fig. 1b) is available at the NCBI Gene Expression Omnibus (GSE37704, accession nos. SRR493366–SRR493371). The GEUVADIS data set is available at the European Nucleotide Archive (accession no. ERP001942). The authors declare no competing financial interests.

Funders:

Funding Agency	Grant Number
NIH	R01 DK094699
NIH	R01 HG006129

Issue or Number:

DOI:

10.1038/nmeth.4324

Record Number:

CaltechAUTHORS:20170612-084553487

Persistent URL:

https://resolver.caltech.edu/CaltechAUTHORS:20170612-084553487

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No commercial reproduction, distribution, display or performance rights in this work are provided.

ID Code:

78089

Collection:

CaltechAUTHORS

Deposited By:

Tony Diaz

Deposited On:

12 Jun 2017 16:04

Last Modified:

15 Nov 2021 17:36

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