README.md
In pachterlab/sleuth: Tools for investigating RNA-Seq

sleuth

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.

Installation

The easiest way to install is using the devtools package through Bioconductor.

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install()
BiocManager::install("devtools")    # only if devtools not yet installed
BiocManager::install("pachterlab/sleuth")

These commands will install sleuth along with all of its dependencies. You can then load sleuth like any other R package:

library('sleuth')

Installation via `conda`

If you have conda, a cross-platform package manager installed, you can install sleuth via the bioconda channel.

conda install --channel bioconda r-sleuth

Documentation

We recommend starting with the vignette:

vignette('intro', package = 'sleuth')

Detailed documentation can be retrieved within R using the help() command:

help(package = 'sleuth')

Specific function documentation can also be accessed using ? as you would for any other function in R:

?sleuth_prep

Conventions

All sleuth "core" functionality is prefixed by sleuth_ (e.g. sleuth_prep()).
All sleuth plots are prefixed with plot_ (e.g. plot_ma())

Further help

Please visit the sleuth website for ways to get help. We have several new walk-throughs at the main sleuth website. In particular, you might find the kallisto-sleuth users Google group helpful.

Please post bug reports on GitHub.