.gitignore
CITATION.cff
DEVELOPING.md
LICENSE
Makefile
README.md
README_old.md
README_pypi.md
VERSION
con_to_ncc.sh
dip-c
nuc_dynamics.sh
pyproject.toml
pytest.ini
.github/workflows/publish.yml
.github/workflows/test.yml
.vscode/settings.json
color/hg19.cg.20k.hom.txt
color/hg19.cg.20k.txt
color/hg19.chr.cen
color/hg19.chr.hom.len
color/hg19.chr.len
color/hg19.chr.txt
color/hg19.cpg.100k.hom.txt
color/hg19.cpg.100k.txt
color/hg19.cpg.1m.hom.txt
color/hg19.cpg.1m.txt
color/hg19.cpg.20k.hom.txt
color/hg19.cpg.20k.rank.txt
color/hg19.cpg.20k.txt
color/hg19.cpg.500k.hom.txt
color/hg19.cpg.500k.txt
color/hg38.chr.len
color/hg38.chr.txt
color/hg38.cpg.100k.txt
color/hg38.cpg.1m.txt
color/hg38.cpg.20k.txt
color/mm10.cg.20k.txt
color/mm10.chr.cen
color/mm10.chr.hom.len
color/mm10.chr.len
color/mm10.chr.txt
color/mm10.cpg.100k.txt
color/mm10.cpg.1m.txt
color/mm10.cpg.20k.txt
images/bincon.png
images/bincon_imputed.png
images/coverage-badge.svg
images/juicebox.png
images/juicebox_imputed.png
images/logo.png
images/logo_small.png
images/pymol.cpg.png
images/pymol.exp.n.label.png
images/pymol.exp.n.png
images/pymol.n.png
patch/README.md
patch/dyn_util.pyx
patch/nuc_dynamics.py
patch/pdbx_reader_escape_sequences.patch
patch/trim.c
pymol/color_centromere.py
pymol/color_centromere_legend.pdf
pymol/color_chromosomes.py
pymol/color_locus_legend.pdf
pymol/color_methylation.py
pymol/color_radial_legend.pdf
pymol/dip_c_color.py
pymol/pymol_ard.py
pymol/pymol_movie_exp.py
pymol/pymol_tad.py
recipes/bioconda/meta.yaml
recipes/dip-c/meta.yaml
release/README.md
release/prepare_release.sh
scripts/cen_to_leg.sh
scripts/cg.sh
scripts/color_chr_len_to_hom.sh
scripts/color_chr_to_hom.sh
scripts/color_to_rank.py
scripts/con_imputed_to_juicer_pre_short.sh
scripts/con_to_juicer_pre_short.sh
scripts/con_to_matlab_human.sh
scripts/con_to_matlab_mouse.sh
scripts/cpg.sh
scripts/hickit_3dg_to_3dg.sh
scripts/hickit_3dg_to_3dg_rescale_backbone.sh
scripts/hickit_3dg_to_3dg_rescale_unit.sh
scripts/hickit_impute_pairs_to_con.sh
scripts/hickit_impute_separated_pairs_to_con.sh
scripts/hickit_pairs_to_con.sh
scripts/name_color_x_y_z_to_cif.py
scripts/network.py
scripts/network_around.py
scripts/snp_sanger_b6_cast.py
scripts/snp_sanger_cast_129s1.py
scripts/snp_sanger_cast_b6.py
scripts/stack_row_np_int.py
scripts/sum_np_int.py
snps/NA12878.txt.gz
src/dip_c/__init__.py
src/dip_c/_version.py
src/dip_c/classes.py
src/dip_c/cli.py
src/dip_c/completion.py
src/dip_c/dip-c.bash-completion
src/dip_c/py.typed
src/dip_c/commands/__init__.py
src/dip_c/commands/align.py
src/dip_c/commands/ard.py
src/dip_c/commands/bincon.py
src/dip_c/commands/clean.py
src/dip_c/commands/clean3.py
src/dip_c/commands/color.py
src/dip_c/commands/color2.py
src/dip_c/commands/con.py
src/dip_c/commands/con3.py
src/dip_c/commands/cv.py
src/dip_c/commands/dedup.py
src/dip_c/commands/dist.py
src/dip_c/commands/exp.py
src/dip_c/commands/force.py
src/dip_c/commands/impute.py
src/dip_c/commands/impute3.py
src/dip_c/commands/info.py
src/dip_c/commands/mgcolor.py
src/dip_c/commands/mkcon.py
src/dip_c/commands/pd.py
src/dip_c/commands/pos.py
src/dip_c/commands/reg.py
src/dip_c/commands/reg3.py
src/dip_c/commands/rg.py
src/dip_c/commands/seg.py
src/dip_c/commands/tad.py
src/dip_c/commands/vis.py
src/dip_c/data/__init__.py
src/dip_c/data/color/hg19.cg.20k.hom.txt.gz
src/dip_c/data/color/hg19.cg.20k.txt.gz
src/dip_c/data/color/hg19.chr.cen.gz
src/dip_c/data/color/hg19.chr.hom.len.gz
src/dip_c/data/color/hg19.chr.len.gz
src/dip_c/data/color/hg19.chr.txt.gz
src/dip_c/data/color/hg19.cpg.100k.hom.txt.gz
src/dip_c/data/color/hg19.cpg.100k.txt.gz
src/dip_c/data/color/hg19.cpg.1m.hom.txt.gz
src/dip_c/data/color/hg19.cpg.1m.txt.gz
src/dip_c/data/color/hg19.cpg.20k.hom.txt.gz
src/dip_c/data/color/hg19.cpg.20k.rank.txt.gz
src/dip_c/data/color/hg19.cpg.20k.txt.gz
src/dip_c/data/color/hg19.cpg.500k.hom.txt.gz
src/dip_c/data/color/hg19.cpg.500k.txt.gz
src/dip_c/data/color/hg38.chr.len.gz
src/dip_c/data/color/hg38.chr.txt.gz
src/dip_c/data/color/hg38.cpg.100k.txt.gz
src/dip_c/data/color/hg38.cpg.1m.txt.gz
src/dip_c/data/color/hg38.cpg.20k.txt.gz
src/dip_c/data/color/mm10.cg.20k.txt.gz
src/dip_c/data/color/mm10.chr.cen.gz
src/dip_c/data/color/mm10.chr.hom.len.gz
src/dip_c/data/color/mm10.chr.len.gz
src/dip_c/data/color/mm10.chr.txt.gz
src/dip_c/data/color/mm10.cpg.100k.txt.gz
src/dip_c/data/color/mm10.cpg.1m.txt.gz
src/dip_c/data/color/mm10.cpg.20k.txt.gz
src/run_dipc.egg-info/PKG-INFO
src/run_dipc.egg-info/SOURCES.txt
src/run_dipc.egg-info/dependency_links.txt
src/run_dipc.egg-info/entry_points.txt
src/run_dipc.egg-info/requires.txt
src/run_dipc.egg-info/top_level.txt
tests/README.md
tests/__init__.py
tests/requirements.txt
tests/run_tests.sh
tests/test_classes.py
tests/test_cli.py
tests/test_commands.py
tests/test_completion.py
tests/test_data.py
tests/data/gm12878_11.clean.chr21_22.con.txt.gz
tests/data/gm12878_11.clean.chr22.con.txt.gz
tests/data/gm12878_11.clean.con.txt.gz
tests/data/gm12878_11.impute.3dg.txt
tests/data/gm12878_11.impute.3dg.txt.gz
tests/data/gm12878_11.impute.chr21_22.3dg.txt
tests/data/gm12878_11.impute.chr21_22.con.txt.gz
tests/data/gm12878_11.impute.chr22.3dg.txt
tests/data/gm12878_11.impute.chr22.3dg.txt.gz
tests/data/gm12878_11.impute.chr22.con.txt.gz
tests/data/gm12878_11.impute.con.txt.gz