This package contains the R code implementing the computational analysis steps, in the form of Rmarkdown documents, that enable readers to reproduce all major figures and results reported in manuscript "Multi-omics reveals clinically relevant proliferative drive associated with mTOR-MYC-OXPHOS activity in chronic lymphocytic leukemia" by Lu and Cannizzaro et al.. In addition, the CLLPDestimate function in the R package can be used to compute CLL-PD from compatible gene expression data provided by users. Instructions can be found in the vignette of the package.
Excuting the R markdown files in this package requires a large collection of packages, which can be quite cumbersome and may reduce reproducibility when the packages update in the future. Therefore we created a docker container for the system environment that is necessary to run all the analysis steps in the R markdown files. The docker container can be found at Docker Hub: https://hub.docker.com/r/lujunyan1118/mofacll
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Install docker on your local computer.
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Run the command below in a terminal.
docker pull lujunyan1118/mofacll
docker run -d -p 8787:8787 -e DISABLE_AUTH=true lujunyan1118/mofacll
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Navigate to http://localhost:8787 in a browser and an R Studio Server interface should appear.
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In the current directory, you should see a folder called "vignettes_standalone", which contains the R Markdown files for reproducing the analysis results.
Note: the last part of the analysis (part6.Rmd) involves a single-cell CyTOF dataset, which requires a relatively large amount of memory. If you experience that the processing of this script fails due to lack of memory, please consider increasing the memory usage limit of the docker container.
Please see https://hub.docker.com/r/rocker/rstudio and https://github.com/rocker-org/rocker/wiki for the additional documentation of the rocker/rstudio container.
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
Email: [email protected]