.gitignore
.readthedocs.yml
.travis.yml
LICENSE
README.rst
requirements.txt
setup.py
brie/__init__.py
brie/settings.py
brie/version.py
brie.egg-info/PKG-INFO
brie.egg-info/SOURCES.txt
brie.egg-info/dependency_links.txt
brie.egg-info/entry_points.txt
brie.egg-info/requires.txt
brie.egg-info/top_level.txt
brie/_cli/__init__.py
brie/_cli/_cli.py
brie/_cli/count.py
brie/_cli/download.py
brie/_cli/extract.py
brie/_cli/quant.py
brie/bin/__init__.py
brie/bin/brie_main.py
brie/bin/count.py
brie/bin/quant.py
brie/models/__init__.py
brie/models/base_model.py
brie/models/hypothesis_tests.py
brie/models/model_Beta.py
brie/models/model_TFProb.py
brie/models/model_TFProb_dev.py
brie/models/model_wrap.py
brie/models/simulator.py
brie/models/tools.py
brie/plot/LRtest_plot.py
brie/plot/__init__.py
brie/plot/base_plot.py
brie/utils/__init__.py
brie/utils/base_utils.py
brie/utils/bias_utils.py
brie/utils/count.py
brie/utils/fasta_utils.py
brie/utils/gtf_utils.py
brie/utils/io_utils.py
brie/utils/preprocessing.py
brie/utils/run_utils.py
brie/utils/sam_utils.py
brie/utils/tran_utils.py
brie/version1/brie.py
brie/version1/brie_diff.py
brie/version1/model_brie.py
doc/Makefile
doc/brie1.rst
doc/brie_count.rst
doc/brie_quant.rst
doc/conf.py
doc/index.rst
doc/install.rst
doc/quick_start.rst
doc/release.rst
doc/requirements.txt
doc/tutorial.rst
examples/Prior_distribution_BRIE2.ipynb
examples/brie2_demo.sh
examples/make_list.sh
examples/demo_v1/anno_maker.sh
examples/demo_v1/brie_demo.sh
examples/gastrulation/E-MTAB-4079.130cells.txt
examples/gastrulation/brie_sashimi.sh
examples/gastrulation/gastrulation_130cells.sh
examples/gastrulation/prepare_anno.sh
examples/gastrulation/sashimi_setting.txt
simulator/README.rst
simulator/simuDropout.py
simulator/simuPSI.py
simulator/spanki_demo.sh
simulator/utils.py