rosace

Update

v1.1: May 30, 2024

• Added options to take out nonsense/stop mutations from position-level estimates
• Fixed a bug in position-level lfsr computation

Overview

rosace is an R package for analyzing growth-based deep mutational scanning screen data.

Installation

rosace uses cmdstanr to run inference. Please ensure that cmdstanr is properly installed before installing rosace. Below is a concise installation command; for complete details, please refer to the official website.

install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))

# use cmdstanr to install CmdStan, this requires a working C++ toolchain and compiler
library(cmdstanr)
install_cmdstan(cores = 4)

To install rosace start R and first install devtools by typing

install.packages("devtools")

and install rosace by typing

devtools::install_github("pimentellab/rosace")

If you prefer to use Docker, we also provide a Docker image for rosace. You can pull the image in the command line with

docker pull cbmacdo/rosace-docker

See the full Installation Instructions for further details and alternative installation options.

Getting started

library("rosace")

We recommend starting with the vignette. A vignette for the simulation module Rosette is also avaliable.

Further help

You may submit a bug report here on GitHub as an issue or you could send an email to roserao@ucla.edu.

Citing rosace

Please cite the following publication if you use rosace: Rao, J., Xin, R., Macdonald, C. et al. Rosace: a robust deep mutational scanning analysis framework employing position and mean-variance shrinkage. Genome Biol 25, 138 (2024). https://doi.org/10.1186/s13059-024-03279-7