fraunhofer-izi / tumor_deconvolution

Tools to infer the immune cell composition of tumor tissue from RNA-seq samples.

Introduction

This is a collection of code that was used for the Ph.D. thesis

Computational Gene Expression Deconvolution

by Dominik J. Otto. This repo only contains the code used in the example application "inference of cell decomposition". The docker container generated by this repo was submitted to the Tumor Deconvolution DREAM Challenge. The code that was applied applied for the deoncolution of expression patterns is collected in another repo.

What to run

Make sure a directory ../data is available. Run everything in main.sh to make the model and docker/Readme to make and upload the docker images.

Dependencies

We us the Slurm Workload Manager to shechule jobs on our cluster system with sbatch. However, all scriptes called with sbatch <script name> can be run without sbatch.

To make R 3.5.2 available we use the Lmod module system. The respective calls source /etc/profile.d/modules.sh and module load R/3.5.2-0 can be omitted if R 3.5.2 is already available.

The calls source ~dominik.otto/enterEnv.sh load a specially build conda environment. If all use python packages are availabe these calls can be omitted.

The python multiprocessing package had a bug not allowing to share files larger than 4GB between the threads. Please make sure this bug is fiexed, e.g., by implementing this PR in your version of multiprocessing: python/cpython#10305

License

Copyright (C) 2019 Fraunhofer-Gesellschaft zur Foerderung der angewandten Forschung e.V. acting on behalf of its Fraunhofer Institute for Cell Therapy and Immunology (IZI).

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 http://www.gnu.org/licenses/.

Citation

BibTeX:

@software{dominik_j_otto_2020_4287137,
  author       = {Dominik J. Otto},
  title        = {fraunhofer-izi/tumor\_deconvolution: v1.0},
  month        = nov,
  year         = 2020,
  publisher    = {Zenodo},
  version      = {v1.0},
  doi          = {10.5281/zenodo.4287137},
  url          = {https://doi.org/10.5281/zenodo.4287137} Titel anhand dieser DOI in Citavi-Projekt übernehmen
}