Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis.
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')
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
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
sleuth_
(e.g.
sleuth_prep()
).plot_
(e.g. plot_ma()
)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 (C) 2015 Harold Pimentel, Nicolas Bray, Pall Melsted, Lior Pachter
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