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Welcome to the RegSeq wiki!
This is a GitHub repository for Reg-Seq, an experimental protocol that determines the binding energy matrix for regulatory regions of the genome. The website for the original Reg-Seq paper can be found here.
The repository is split into four main directories, many of which have
subdirectories. This structure has been designed to be easily navigable by
humans and computers alike, allowing for rapid location of specific files and
instructions. Within each directory is a README.md file which summarizes the
purpose of that directory as well as some examples where necessary.
code contains Jupyter notebooks to perform computational steps of the Reg-Seq protocol from start to finish. Where all of the executed code lives. This includes pipelines, scripts, and
figure files.
data contains prior data files, such as designed sequences, negative controls, or output analysis files.
protocol contains MarkDown files that outline each step to perform Reg-Seq in total.
RegSeq contains Python files which can be easily executed to perform your own analyses.
In order to use the functions within the RegSeq module it is necessary to
install the package locally. This can simply be done by navigating in the
terminal to the main project directory and typing the command
pip install -e ./
The 'setup.py' file will take care of the installation. The -e option within
the package allows for the constant update of the package as it might be
subject to changes as the project is being developed.
The modules contained in the package include:
module1.py : explanation here.
module1.py : explanation here.
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