sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live. The sleuth methods are described in
H Pimentel, NL Bray, S Puente, P Melsted and Lior Pachter, Differential analysis of RNA-seq incorporating quantification uncertainty, Nature Methods (2017), advanced access.
Scripts reproducing all the results of the paper are available here.
The easiest way to install is using the
devtools package through Bioconductor.
source("http://bioconductor.org/biocLite.R") biocLite("devtools") # only if devtools not yet installed biocLite("pachterlab/sleuth")
These commands will install
sleuth along with all of its dependencies. You
can then load
sleuth like any other R package:
conda install --channel bioconda r-sleuth
We recommend starting with the vignette:
vignette('intro', package = 'sleuth')
Detailed documentation can be retrieved within R using the
help(package = 'sleuth')
Specific function documentation can also be accessed using
? as you would for
any other function in R:
- All sleuth "core" functionality is prefixed by
- All sleuth plots are prefixed with
Please post bug reports on GitHub.
Copyright (C) 2017 Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter