├── .gitignore ├── LICENSE ├── README.md ├── array_tools.py ├── data_tools.py ├── hic_oe.py ├── linear_algebra.py ├── minimds.py ├── minimds_inter.py ├── plotting.py ├── requirements.txt ├── scripts ├── README.txt ├── bin_bed.py ├── chrom_from_tar.sh ├── chromosome3d_input.py ├── chromsde_input.py ├── distance_decay.py ├── figures │ ├── fig1.py │ ├── fig1.sh │ ├── fig10.py │ ├── fig10.sh │ ├── fig2.py │ ├── fig2.sh │ ├── fig4.py │ ├── fig4.sh │ ├── fig5.py │ ├── fig5.sh │ ├── fig6.py │ ├── fig6.sh │ ├── fig7.py │ ├── fig7.sh │ ├── fig8.py │ ├── fig8.sh │ ├── fig9.py │ ├── fig9.sh │ ├── sup1.py │ ├── sup1.sh │ ├── sup2.py │ ├── sup2.sh │ ├── sup3.py │ └── sup3.sh ├── get_chrom_sizes.py ├── get_gm12878.sh ├── get_gm12878_inter.sh ├── heatmap.py ├── hicpro │ ├── HindIII_resfrag_hg19_downsampled.bed │ ├── hic.matrix │ ├── hicpro_interchromosomal.sh │ └── hicpro_to_bedpe.py ├── hsa_input.py ├── install_chromosome3d.sh ├── install_chromsde.sh ├── install_hsa.sh ├── install_mogen.sh ├── misc.py ├── mogen_input.py ├── normalize.py ├── normalize.sh ├── parameters │ ├── parameters_chr10_10kb.txt │ ├── parameters_chr11_10kb.txt │ ├── parameters_chr12_10kb.txt │ ├── parameters_chr13_10kb.txt │ ├── parameters_chr14_10kb.txt │ ├── parameters_chr15_10kb.txt │ ├── parameters_chr16_10kb.txt │ ├── parameters_chr17_10kb.txt │ ├── parameters_chr18_10kb.txt │ ├── parameters_chr19_10kb.txt │ ├── parameters_chr1_10kb.txt │ ├── parameters_chr20_10kb.txt │ ├── parameters_chr21_10kb.txt │ ├── parameters_chr22_100kb.txt │ ├── parameters_chr22_10kb.txt │ ├── parameters_chr2_10kb.txt │ ├── parameters_chr3_10kb.txt │ ├── parameters_chr4_10kb.txt │ ├── parameters_chr5_10kb.txt │ ├── parameters_chr6_10kb.txt │ ├── parameters_chr7_10kb.txt │ ├── parameters_chr8_10kb.txt │ ├── parameters_chr9_10kb.txt │ └── parameters_chrX_10kb.txt ├── run_chromsde.m ├── run_chromsde_100kb.m ├── run_chromsde_rep1.m ├── run_chromsde_rep2.m ├── simple_tad.py ├── struct_to_pdb.py ├── structure_to_xyz.sh └── test.sh ├── tad.py └── tools.py /.gitignore: -------------------------------------------------------------------------------- 1 | *.pyc 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/README.md -------------------------------------------------------------------------------- /array_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/array_tools.py -------------------------------------------------------------------------------- /data_tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/data_tools.py -------------------------------------------------------------------------------- /hic_oe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/hic_oe.py -------------------------------------------------------------------------------- /linear_algebra.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/linear_algebra.py -------------------------------------------------------------------------------- /minimds.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/minimds.py -------------------------------------------------------------------------------- /minimds_inter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/minimds_inter.py -------------------------------------------------------------------------------- /plotting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/plotting.py -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/requirements.txt -------------------------------------------------------------------------------- /scripts/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/README.txt -------------------------------------------------------------------------------- /scripts/bin_bed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/bin_bed.py -------------------------------------------------------------------------------- /scripts/chrom_from_tar.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/chrom_from_tar.sh -------------------------------------------------------------------------------- /scripts/chromosome3d_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/chromosome3d_input.py -------------------------------------------------------------------------------- /scripts/chromsde_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/chromsde_input.py -------------------------------------------------------------------------------- /scripts/distance_decay.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/distance_decay.py -------------------------------------------------------------------------------- /scripts/figures/fig1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig1.py -------------------------------------------------------------------------------- /scripts/figures/fig1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig1.sh -------------------------------------------------------------------------------- /scripts/figures/fig10.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig10.py -------------------------------------------------------------------------------- /scripts/figures/fig10.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig10.sh -------------------------------------------------------------------------------- /scripts/figures/fig2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig2.py -------------------------------------------------------------------------------- /scripts/figures/fig2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig2.sh -------------------------------------------------------------------------------- /scripts/figures/fig4.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig4.py -------------------------------------------------------------------------------- /scripts/figures/fig4.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig4.sh -------------------------------------------------------------------------------- /scripts/figures/fig5.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig5.py -------------------------------------------------------------------------------- /scripts/figures/fig5.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig5.sh -------------------------------------------------------------------------------- /scripts/figures/fig6.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig6.py -------------------------------------------------------------------------------- /scripts/figures/fig6.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig6.sh -------------------------------------------------------------------------------- /scripts/figures/fig7.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig7.py -------------------------------------------------------------------------------- /scripts/figures/fig7.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig7.sh -------------------------------------------------------------------------------- /scripts/figures/fig8.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig8.py -------------------------------------------------------------------------------- /scripts/figures/fig8.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig8.sh -------------------------------------------------------------------------------- /scripts/figures/fig9.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig9.py -------------------------------------------------------------------------------- /scripts/figures/fig9.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/fig9.sh -------------------------------------------------------------------------------- /scripts/figures/sup1.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/sup1.py -------------------------------------------------------------------------------- /scripts/figures/sup1.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/sup1.sh -------------------------------------------------------------------------------- /scripts/figures/sup2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/sup2.py -------------------------------------------------------------------------------- /scripts/figures/sup2.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/sup2.sh -------------------------------------------------------------------------------- /scripts/figures/sup3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/sup3.py -------------------------------------------------------------------------------- /scripts/figures/sup3.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/figures/sup3.sh -------------------------------------------------------------------------------- /scripts/get_chrom_sizes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/get_chrom_sizes.py -------------------------------------------------------------------------------- /scripts/get_gm12878.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/get_gm12878.sh -------------------------------------------------------------------------------- /scripts/get_gm12878_inter.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/get_gm12878_inter.sh -------------------------------------------------------------------------------- /scripts/heatmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/heatmap.py -------------------------------------------------------------------------------- /scripts/hicpro/HindIII_resfrag_hg19_downsampled.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/hicpro/HindIII_resfrag_hg19_downsampled.bed -------------------------------------------------------------------------------- /scripts/hicpro/hic.matrix: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/hicpro/hic.matrix -------------------------------------------------------------------------------- /scripts/hicpro/hicpro_interchromosomal.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/hicpro/hicpro_interchromosomal.sh -------------------------------------------------------------------------------- /scripts/hicpro/hicpro_to_bedpe.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/hicpro/hicpro_to_bedpe.py -------------------------------------------------------------------------------- /scripts/hsa_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/hsa_input.py -------------------------------------------------------------------------------- /scripts/install_chromosome3d.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/install_chromosome3d.sh -------------------------------------------------------------------------------- /scripts/install_chromsde.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/install_chromsde.sh -------------------------------------------------------------------------------- /scripts/install_hsa.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/install_hsa.sh -------------------------------------------------------------------------------- /scripts/install_mogen.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/install_mogen.sh -------------------------------------------------------------------------------- /scripts/misc.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/misc.py -------------------------------------------------------------------------------- /scripts/mogen_input.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/mogen_input.py -------------------------------------------------------------------------------- /scripts/normalize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/normalize.py -------------------------------------------------------------------------------- /scripts/normalize.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/normalize.sh -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr10_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr10_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr11_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr11_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr12_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr12_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr13_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr13_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr14_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr14_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr15_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr15_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr16_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr16_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr17_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr17_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr18_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr18_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr19_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr19_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr1_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr1_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr20_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr20_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr21_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr21_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr22_100kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr22_100kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr22_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr22_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr2_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr2_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr3_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr3_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr4_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr4_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr5_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr5_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr6_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr6_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr7_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr7_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr8_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr8_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chr9_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chr9_10kb.txt -------------------------------------------------------------------------------- /scripts/parameters/parameters_chrX_10kb.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/parameters/parameters_chrX_10kb.txt -------------------------------------------------------------------------------- /scripts/run_chromsde.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/run_chromsde.m -------------------------------------------------------------------------------- /scripts/run_chromsde_100kb.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/run_chromsde_100kb.m -------------------------------------------------------------------------------- /scripts/run_chromsde_rep1.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/run_chromsde_rep1.m -------------------------------------------------------------------------------- /scripts/run_chromsde_rep2.m: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/run_chromsde_rep2.m -------------------------------------------------------------------------------- /scripts/simple_tad.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/simple_tad.py -------------------------------------------------------------------------------- /scripts/struct_to_pdb.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/struct_to_pdb.py -------------------------------------------------------------------------------- /scripts/structure_to_xyz.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/structure_to_xyz.sh -------------------------------------------------------------------------------- /scripts/test.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/scripts/test.sh -------------------------------------------------------------------------------- /tad.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/tad.py -------------------------------------------------------------------------------- /tools.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/seqcode/miniMDS/HEAD/tools.py --------------------------------------------------------------------------------