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figures
figures
 
 
hicpro
hicpro
 
 
parameters
parameters
 
 
README.txt
README.txt
 
 
bin_bed.py
bin_bed.py
 
 
chrom_from_tar.sh
chrom_from_tar.sh
 
 
chromosome3d_input.py
chromosome3d_input.py
 
 
chromsde_input.py
chromsde_input.py
 
 
distance_decay.py
distance_decay.py
 
 
get_chrom_sizes.py
get_chrom_sizes.py
 
 
get_gm12878.sh
get_gm12878.sh
 
 
get_gm12878_inter.sh
get_gm12878_inter.sh
 
 
heatmap.py
heatmap.py
 
 
hsa_input.py
hsa_input.py
 
 
install_chromosome3d.sh
install_chromosome3d.sh
 
 
install_chromsde.sh
install_chromsde.sh
 
 
install_hsa.sh
install_hsa.sh
 
 
install_mogen.sh
install_mogen.sh
 
 
misc.py
misc.py
 
 
mogen_input.py
mogen_input.py
 
 
normalize.py
normalize.py
 
 
normalize.sh
normalize.sh
 
 
run_chromsde.m
run_chromsde.m
 
 
run_chromsde_100kb.m
run_chromsde_100kb.m
 
 
run_chromsde_rep1.m
run_chromsde_rep1.m
 
 
run_chromsde_rep2.m
run_chromsde_rep2.m
 
 
simple_tad.py
simple_tad.py
 
 
struct_to_pdb.py
struct_to_pdb.py
 
 
structure_to_xyz.sh
structure_to_xyz.sh
 
 
test.sh
test.sh
 
 

README.txt

Run the bash scripts to recreate the figures from the paper. 

For example, fig1.sh will create the files Fig1A.png and Fig1B.png. sup1.sh will create supplemental fig. 1. 

Requirements:
	- matplotlib
	- scipy
	- MOGEN requires Java
	- ChromSDE requires MATLAB
	- HSA requires R

Chromosome3D can't be installed programmatically, so it must be installed according to the instructions here (https://github.com/multicom-toolbox/Chromosome3D) prior to running fig4.sh, fig5.sh, sup1.sh, sup2.sh, or sup3.sh. 

4/6/17: The ChromSDE website is currently inaccessible. Relevant portions of code have been commented out.