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DIRECTORY STRUCTURE:
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data:
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This is were all data are stored/saved.
run get_data.sh in order to automatically
download and extract data needed in order
to start the project.
These data include:
- contact_maps: The raw full contact maps
- edges: contact results of thresholding contact maps.
- graphlets: extracted orbits from edges.
- orbits: orbits ordered so they can be served as input for correlation procedures
- loci
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external:
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Contains scripts and binaries from other languages
than python that are required in this project.
The main ones include the 'orca' package in R
programming language that can be installed
using install.packages('orca') in R.
Also a java jar file is used to calculate
MIC values from orbit information.
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notebooks
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Contains jupyter notebooks for a demo of
what we did in the project
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requirements.txt
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run 'pip -r requirements.txt' in order to
install all pre-requisite packages in python.
Also, you need to install iced package
manually in python, which can be downloaded
from here:
https://graphiclet.localtunnel.me/secret/iced.zip