LICENSE.txt
MANIFEST.in
README.rst
ez_setup.py
requirements.txt
setup.cfg
setup.py
./hifive/__init__.py
./hifive/fend.py
./hifive/fivec.py
./hifive/fivec_binning.py
./hifive/fivec_data.py
./hifive/fragment.py
./hifive/hic.py
./hifive/hic_binning.py
./hifive/hic_data.py
./hifive/hic_domains.py
./hifive/plotting.py
./hifive/quasar.py
./hifive/schic.py
./hifive/version.py
./hifive.egg-info/PKG-INFO
./hifive.egg-info/SOURCES.txt
./hifive.egg-info/dependency_links.txt
./hifive.egg-info/not-zip-safe
./hifive.egg-info/requires.txt
./hifive.egg-info/top_level.txt
./hifive/commands/__init__.py
./hifive/commands/combine_fivec_replicates.py
./hifive/commands/combine_hic_replicates.py
./hifive/commands/complete_fivec_project.py
./hifive/commands/complete_hic_project.py
./hifive/commands/connect_files.py
./hifive/commands/create_fendset.py
./hifive/commands/create_fivec_dataset.py
./hifive/commands/create_fivec_heatmap.py
./hifive/commands/create_fivec_project.py
./hifive/commands/create_fragmentset.py
./hifive/commands/create_hic_dataset.py
./hifive/commands/create_hic_heatmap.py
./hifive/commands/create_hic_mrheatmap.py
./hifive/commands/create_hic_project.py
./hifive/commands/find_quasar_scores.py
./hifive/commands/get_fivec_interval.py
./hifive/commands/get_hic_interval.py
./hifive/commands/normalize_fivec_project.py
./hifive/commands/normalize_hic_project.py
./hifive/libraries/__init__.py
./hifive/libraries/hmm.py
bin/fetch_mrh_data
bin/hifive
doc/Makefile
doc/api.rst
doc/binning.rst
doc/conf.py
doc/distance_dependence.rst
doc/fend.rst
doc/filtering_data.rst
doc/fivec.rst
doc/fivec_binning.rst
doc/fivec_data.rst
doc/fivec_tutorial.rst
doc/fragment.rst
doc/fragment_handling.rst
doc/getting_started.rst
doc/hic.rst
doc/hic_binning.rst
doc/hic_data.rst
doc/hic_tutorial.rst
doc/hifive.rst
doc/index.rst
doc/introduction.rst
doc/loading_data.rst
doc/mrheatmap.rst
doc/normalization.rst
doc/plotting.rst
doc/quasar.rst
doc/quasar_scoring.rst
doc/release_history.rst
doc/_static/5c_distance.png
doc/_static/flowchart.png
doc/_static/hic_distance.png
doc/_static/hic_filter.png
hifive/libraries/_fivec_binning.pyx
hifive/libraries/_fivec_optimize.pyx
hifive/libraries/_hic_binning.pyx
hifive/libraries/_hic_distance.pyx
hifive/libraries/_hic_domains.pyx
hifive/libraries/_hic_interactions.pyx
hifive/libraries/_hic_optimize.pyx
hifive/libraries/_hmm.pyx
hifive/libraries/_normal.cpp
hifive/libraries/_normal.hpp
hifive/libraries/_quasar.pyx
test/test_fend.py
test/test_fivec_binning.py
test/test_fivec_data.py
test/test_fivec_project.py
test/test_frag.py
test/test_hic_binning.py
test/test_hic_data.py
test/test_hic_project.py
test/data/test.counts
test/data/test.counts_full
test/data/test.fcd
test/data/test.fch
test/data/test.fcp
test/data/test.fends
test/data/test.frags
test/data/test.hcd
test/data/test.hch
test/data/test.hcp
test/data/test.len
test/data/test.mat
test/data/test.raw
test/data/test_bin.fends
test/data/test_bin.hcd
test/data/test_bin.hcp
test/data/test_bin_express.hcp
test/data/test_binned.fends
test/data/test_binned.hdf5
test/data/test_binning.fcp
test/data/test_binning.hcp
test/data/test_express.fcp
test/data/test_express.hcp
test/data/test_fend.bed
test/data/test_fivec_1.bam
test/data/test_fivec_1.sam
test/data/test_fivec_2.bam
test/data/test_fivec_2.sam
test/data/test_frag.bed
test/data/test_full.mat
test/data/test_hic_1.bam
test/data/test_hic_2.bam
test/data/test_import.fcd
test/data/test_import_bam.hcd
test/data/test_import_bin_bam.hcd
test/data/test_import_bin_mat.hcd
test/data/test_import_bin_raw.hcd
test/data/test_import_mat.hcd
test/data/test_import_matrix.hcd
test/data/test_import_raw.hcd
test/data/test_len.fends
test/data/test_probability.fcp
test/data/test_probbin.hcp
test/data/test_probpois.hcp