Mitra S., Zhong J., Tran T.Q., MacAlpine D.M., Hartemink A.J. (2021) RoboCOP: jointly computing chromatin occupancy profiles for numerous factors from chromatin accessibility data. Nucleic Acids Research, vol 49. https://doi.org/10.1093/nar/gkab553
Mitra S., Zhong J., MacAlpine D.M., Hartemink A.J. (2020) RoboCOP: Multivariate State Space Model Integrating Epigenomic Accessibility Data to Elucidate Genome-Wide Chromatin Occupancy. In: Schwartz R. (eds) Research in Computational Molecular Biology. RECOMB 2020. Lecture Notes in Computer Science, vol 12074. Springer, Cham. https://doi.org/10.1007/978-3-030-45257-5_9
Multivariate state space model that integrates nucleotide sequence and chromatin accessibility data (currently uses only with MNase-seq or ATAC-seq) to compute genome-wide probabilistic occupancy landscape of nucleosomes and transciption factors (collectively known as DNA-binding factors or DBFs).
The list of required python and R modules can be found in robocop-spec-file.txt.
A conda environment can be created using robocop-spec-file.txt as:
conda create --name robocop-env --file robocop-spec-file.txt
conda activate robocop-env
Download RoboCOP from Github.
git clone https://github.com/HarteminkLab/RoboCOP.git
Change to RoboCOP directory and generate the shared object librobocop.so.
cd RoboCOP
cd robocop
bash gccCompile # generates shared library librobocop.so
ls "`pwd`/librobocop.so" # display absolute path of librobocop.so; copy path
Add path of shared library to your configuration file. Example configuration file provided in analysis directory (config_example.ini). So from the robocop directory:
cd ../../analysis/
Open file config_example.ini in an editor and paste path to cshared. For example if path is /home/myhome/RoboCOP/pkg/robocop/librobocop.so then in config.ini set:
cshared=/home/myhome/RoboCOP/pkg/robocop/librobocop.so
Introductory vignette describing how to run RoboCOP can be found here in a jupyter notebook format in the analysis directory.
Vignette describing how to run DynaCOP can be found here in a jupyter notebook format in the analysis directory. The figures from the paper can be generated using dynacop_figures.ipynb.