GitHub - bxlab/HiFive_Paper: All of the scripts necessary to produce the analyses performed in the HiFive paper.

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All of the scripts necessary to produce the analyses performed in the HiFive paper.

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Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
Data/FiveC/Data		Data/FiveC/Data
Figures		Figures
Makefiles		Makefiles
Scripts		Scripts
Settings		Settings
.gitignore		.gitignore
LICENSE		LICENSE
Makefile		Makefile
README.txt		README.txt

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This archive contains all of the scripts used to perform the analyses detailed in the HiFive paper.

To run this, you can simply set the needed paths in the 'dependencies.txt' file in the 'Settings' folder and then use the command 'make all' in the top-level folder. Please note that this will take a long time.

In order for everything to work, you must have several packages and programs already installed. These include:

Libraries:
hdf5

Python packages:
numpy
scipy
h5py
statsmodels

Programs:
samtools
bowtie
R (2.*)

R packages:
maxLik
Rsge
R.utils