Skip to content
sleuth workflow for processing zika RNA-seq dataset
R HTML
Branch: master
Clone or download

Latest commit

Fetching latest commit…
Cannot retrieve the latest commit at this time.

Files

Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
R
inst
kallisto_output
man
tests
vignettes
.gitignore
.lintr
CONTRIBUTING.md
DESCRIPTION
LICENSE
NAMESPACE
README.md
analyze_data.R
zikadesignmatrix.txt

README.md

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

You can’t perform that action at this time.