.gitattributes
.gitignore
.travis.yml
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.py
example/example.py
example/4DN/README.md
example/4DN/cell_19388_500k_pad1_std1_rp0.5_sqrtvc_u8_nn25.label.png
example/4DN/code/raw2mat.py
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A10-AD006.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A10-AD007.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A10-AD008.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A10-AD010.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A10-AD012.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A11-AD001.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A11-AD002.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A11-AD004.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A11-AD006.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A11-AD008.3C.contact.tsv.gz
example/contacts/CEMBA191126_9J_1-CEMBA191126_9J_2-A11-AD010.3C.contact.tsv.gz
example/contacts/contact_table.txt
example/contacts/mm10.main.nochrM.chrom.sizes
example/contacts/test_scool.sh
example/humanPFC/README.md
example/humanPFC/cell_4238_meta_cluster.txt
example/humanPFC/plot/L23_100k_pad1_std1_rp0.5_sqrtvc.covgroup.corr_pc1.png
example/humanPFC/plot/L23_10k_pad2_std1_rp0.5_sqrtvc_dist_trim.covgroup.loop.png
example/humanPFC/plot/L23_25k_pad2_std1_rp0.5_sqrtvc.covgroup.boundprob.w10.png
example/humanPFC/plot/cell_4238_100k_pad1_std1_rp0.5_sqrtvc_dim15_cpgcomp.batch_cluster.png
example/humanPFC/plot/cell_4238_100k_pad1_std1_rp0.5_sqrtvc_dist10M_u15.batch_cluster.png
example/humanPFC/plot/cell_4238_25k_pad2_std1_rp0.5_sqrtvc_boundary_w10_colsum5_logzscore2_tfidf_u15.batch_cluster.png
example/humanPFC/plot/cell_4238_25k_pad2_std1_rp0.5_sqrtvc_dim15_ins.batch_cluster.png
example/plot/Introduction.png
example/plot/framework.png
files/hg19.autosomal.chrom.sizes
files/hg19.autosomal.split10k.chrom.sizes
files/hg38.autosomal.chrom.sizes
files/hg38.autosomal.split10k.chrom.sizes
schicluster/__init__.py
schicluster/__main__.py
schicluster/_hicluster_internal.py
schicluster/_version.py
schicluster/call_domain.R
schicluster/schicluster.py
schicluster.egg-info/PKG-INFO
schicluster.egg-info/SOURCES.txt
schicluster.egg-info/dependency_links.txt
schicluster.egg-info/entry_points.txt
schicluster.egg-info/requires.txt
schicluster.egg-info/top_level.txt
schicluster/compartment/__init__.py
schicluster/compartment/call_compartment.py
schicluster/cool/__init__.py
schicluster/cool/scool.py
schicluster/cool/utilities.py
schicluster/dev/__init__.py
schicluster/dev/concat_cell.py
schicluster/dev/generate_matrix.py
schicluster/dev/imputecell.py
schicluster/dev/loop_sc.py
schicluster/dev/merge_cell.py
schicluster/domain/TopDom.R
schicluster/domain/__init__.py
schicluster/domain/call_domain.py
schicluster/draft/comp_concatcell_chr.py
schicluster/draft/comp_cpg_cell.py
schicluster/draft/domain_concatcell_chr.py
schicluster/draft/domain_insulation_cell.py
schicluster/draft/domain_topdom_cell.R
schicluster/draft/embed_concatcell_chr.py
schicluster/draft/embed_mergechr.py
schicluster/draft/generatematrix_cell.py
schicluster/draft/impute_cell.py
schicluster/draft/loop_bkg_cell.py
schicluster/draft/loop_mergechr.py
schicluster/draft/loop_sumcell_chr.py
schicluster/embedding/__init__.py
schicluster/embedding/calc_embedding.py
schicluster/impute/__init__.py
schicluster/impute/impute.Snakefile
schicluster/impute/impute_chromosome.py
schicluster/impute/merge_cell_to_group.py
schicluster/impute/snakemake.py
schicluster/loop/__init__.py
schicluster/loop/generate_matrix_chunk.Snakefile
schicluster/loop/generate_matrix_group.Snakefile
schicluster/loop/loop_bkg.py
schicluster/loop/loop_calling.py
schicluster/loop/merge_cell_to_group.py
schicluster/loop/snakemake.py