sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. sleuth provides tools for exploratory data analysis utilizing Shiny by RStudio, and implements statistical algorithms for differential analysis that leverage the boostrap estimates of kallisto. A companion blogpost has more information about sleuth.
The sleuth project was developed by Harold Pimentel with assistance from Nicolas Bray, Suzette Puente, Páll Melsted and Lior Pachter. A paper with more details about the program is available from the Nature Methods:
Harold J. Pimentel, Nicolas Bray, Suzette Puente, Páll Melsted and Lior Pachter, Differential analysis of RNA-Seq incorporating quantification uncertainty, Nature Methods (2017), advanced access http://dx.doi.org/10.1038/nmeth.4324.
To see sleuth live in action, check out the lair.