sleuth pipeline

sleuth specifications

Information


Unique identifier OMICS_14127
Name sleuth
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.28.1
Stability Stable
Requirements methods, ggplot2, dplyr
Maintained Yes

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Maintainer


  • person_outline Lior Pachter <>

Publication for sleuth

sleuth IN pipeline

2017
PMCID: 5592924
PMID: 28751504
DOI: 10.1534/g3.117.300080

[…] kallisto was run in single-end read mode, setting the average fragment length of 200bp, and a standard deviation of 60bp for all samples. differential expression analysis was performed using sleuth (pimentel et al. 2016). the following general linear model (glm) was fitted:log(yi)=β0,i+βg,i⋅g+βa,i⋅a+βa::g,i⋅a⋅g,where yi is the tpm count for the ith gene; β0,i is the intercept for the ith […]

sleuth institution(s)
Department of Computer Science, UC Berkeley, Berkeley, CA, USA; Innovative Genomics Initiative, UC Berkeley, Berkeley, CA, USA; Department of Statistics, UC Berkeley, Berkeley, CA, USA; Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavík, Iceland; Departments of Mathematics and Molecular and Cell Biology, UC Berkeley, Berkeley, CA, USA
sleuth funding source(s)
This project was supported by the NIH R01 DK094699 and NIH R01 HG006129.

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