The prerequisites for LeafCutter are
To download the code (you’ll need this for the leafcutter scripts)
git clone https://github.com/davidaknowles/leafcutterIf you just want to get leafcutter quantifications (junction counts for each splicing cluster) e.g. for sQTL analysis, then you just need the python scripts in scripts and clustering.
If you want to do differential splicing analysis and visualization you’ll need to install the leafcutter R package.
Leafcutter relies on stan and its R interface rstan. Installing this can be tricky. If you’re lucky
install.packages("rstan")will just work for you. If not, there are instructions that should help you. On Linux I seem to need
CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX14=g++in ~/.R/Makevars.
For now we also need a version of rstantools (2.0.0) that is not yet on CRAN, so do:
if (!require("devtools")) install.packages("devtools", repos='http://cran.us.r-project.org')
devtools::install_github("stan-dev/rstantools")You can use remotes instead of devtools if you don’t want to wait on the long devtools install.
To compile the R package to perform differential splicing analysis and make junction plots we recommend you install using devtools (this should install the required R package dependencies for you).
devtools::install_github("davidaknowles/leafcutter/leafcutter")We’ve had a report (thanks to Peter Carbonetto) that it may be necessary to restart R before trying to load leafcutter because dplyr may get updated during the installation process.
Alternatively you can install from source. You’ll need to manually install the following R packages: Rcpp, rstan, rstantools, foreach, ggplot2, R.utils, gridExtra, reshape2, Hmisc, dplyr, doMC, optparse, shiny, intervals, shinycssloaders, DT, gtable, shinyjs, DirichletMultinomial, TailRank, magrittr, stringr. Then make sure you’re in the leafcutter package sub-directory (you should see subdirectories called src, R, tests etc) and run
R CMD INSTALL --build .If you see errors try installing the roxygen2 package and running
R CMD INSTALL --preclean --build .which will attempt to use stan to rebuild the C++ code from the .stan files in exec.
If you are a 64-bit Linux conda user ( installation instructions ) we have an experimental package which can be installed using
conda install -c davidaknowles r-leafcutterWe will build macOS and Windows packages if there is demand for this.