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Pascal Sturmfels


Studying computer science at University of Michigan; interests include machine learning in medicine, approximation algorithms, and iOS development.


Sleuth

Sleuth Sleuth is an RNA-seq tool that performs differential expression analysis on quantified reads from kallisto. Sleuth is novel both in its use of statistical bootstraps to understand differential gene expression, and in its use of Shiny to provide in-browser, interactive analyses of RNA-seq experiments. If you are interested in using sleuth, see the sleuth homepage If you would like to see an example of a live sleuth analysis, see the Lair.

RNA-Sequencing, or RNA-seq for short, is a type of study that aims, at a high level, to understand gene expression within an organism. RNA-seq is used to analyze the transcriptome: the parts of the genome that are being expressed by each cell. Unlike the genome, the transcriptome is constantly changing and varies depending on which cell you look at.

RNA-seq helps us understand how environmental factors impact our transcriptome. A better understanding of our transcriptome may help us develop cures or treatments for diseases and medical conditions that currently have no tractable cure.

My role in this project was twofold: I designed several of the data visualizations present in the Sleuth live app, and I made it possible for high-volume Sleuth objects to be shared online.

Sleuth was developed by the Pachter Lab at UC Berkeley.