jasonjwilliamsny / zika

sleuth workflow for processing zika RNA-seq dataset

sleuth: inspect your RNA-Seq

Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis.

Installation

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:

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. In particular, you might find the kallisto-sleuth users Google group helpful.

Please post bug reports on GitHub.

Copyright

Copyright (C) 2015 Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter