Differential analysis of RNA-seq incorporating quantification uncertainty

Harold Pimentel; Nicolas L. Bray; Suzette Puente; Páll Melsted; Lior Pachter

doi:10.1038/nmeth.4324

Differential analysis of RNA-seq incorporating quantification uncertainty

Harold Pimentel, Nicolas L. Bray, Suzette Puente, Páll Melsted, Lior Pachter^*

^*Corresponding author for this work

Faculty of Industrial Engineering, Mechanical Engineering and Computer Science

Research output: Contribution to journal › Article › peer-review

487 Citations (Scopus)

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.

Original language	English
Pages (from-to)	687-690
Number of pages	4
Journal	Nature Methods
Volume	14
Issue number	7
DOIs	https://doi.org/10.1038/nmeth.4324
Publication status	Published - 29 Jun 2017

Bibliographical note

Publisher Copyright:
© 2017 Nature America, Inc., part of Springer Nature. All rights reserved.

Access to Document

10.1038/nmeth.4324

Cite this

@article{f70bf238bf364e768c0778ce41c23f0c,

title = "Differential analysis of RNA-seq incorporating quantification uncertainty",

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.",

author = "Harold Pimentel and Bray, {Nicolas L.} and Suzette Puente and P{\'a}ll Melsted and Lior Pachter",

year = "2017",

month = jun,

day = "29",

doi = "10.1038/nmeth.4324",

language = "English",

volume = "14",

pages = "687--690",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

number = "7",

}

TY - JOUR

T1 - Differential analysis of RNA-seq incorporating quantification uncertainty

AU - Pimentel, Harold

AU - Bray, Nicolas L.

AU - Puente, Suzette

AU - Melsted, Páll

AU - Pachter, Lior

PY - 2017/6/29

Y1 - 2017/6/29

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85026609868&partnerID=8YFLogxK

U2 - 10.1038/nmeth.4324

DO - 10.1038/nmeth.4324

M3 - Article

C2 - 28581496

AN - SCOPUS:85026609868

VL - 14

SP - 687

EP - 690

JO - Nature Methods

JF - Nature Methods

SN - 1548-7091

IS - 7

ER -

Differential analysis of RNA-seq incorporating quantification uncertainty

Abstract

Bibliographical note

Access to Document

Fingerprint

Cite this