.gitignore
LICENSE
README.rst
pyproject.toml
.github/workflows/codeql.yml
.github/workflows/python-publish-toml.yml
data/small_for_test/design.tsv
data/small_for_test/log_normalized_matrix.tsv
data/small_for_test/matrix.tsv
data/small_for_test/normalized_matrix.tsv
data/small_genome/Homo_sapiens.GRCh38.84.reduce.gff3
data/small_genome/Homo_sapiens.GRCh38.84.reduce2.gff3
data/small_leucegene/5_inv16_vs_5/design.tsv
data/small_leucegene/kallisto/01H001/abundance.h5
data/small_leucegene/kallisto/01H001/abundance.tsv
data/small_leucegene/kallisto/01H001/run_info.json
data/small_leucegene/kallisto/01H002/abundance.h5
data/small_leucegene/kallisto/01H002/abundance.tsv
data/small_leucegene/kallisto/01H002/run_info.json
data/small_leucegene/kallisto/02H003/abundance.h5
data/small_leucegene/kallisto/02H003/abundance.tsv
data/small_leucegene/kallisto/02H003/run_info.json
data/small_leucegene/kallisto/02H009/abundance.h5
data/small_leucegene/kallisto/02H009/abundance.tsv
data/small_leucegene/kallisto/02H009/run_info.json
data/small_leucegene/kallisto/02H017/abundance.h5
data/small_leucegene/kallisto/02H017/abundance.tsv
data/small_leucegene/kallisto/02H017/run_info.json
data/small_leucegene/kallisto/03H095/abundance.h5
data/small_leucegene/kallisto/03H095/abundance.tsv
data/small_leucegene/kallisto/03H095/run_info.json
data/small_leucegene/kallisto/03H109/abundance.h5
data/small_leucegene/kallisto/03H109/abundance.tsv
data/small_leucegene/kallisto/03H109/run_info.json
data/small_leucegene/kallisto/03H112/abundance.h5
data/small_leucegene/kallisto/03H112/abundance.tsv
data/small_leucegene/kallisto/03H112/run_info.json
data/small_leucegene/kallisto/04H030/abundance.h5
data/small_leucegene/kallisto/04H030/abundance.tsv
data/small_leucegene/kallisto/04H030/run_info.json
data/small_leucegene/kallisto/04H061/abundance.h5
data/small_leucegene/kallisto/04H061/abundance.tsv
data/small_leucegene/kallisto/04H061/run_info.json
doc/Makefile
doc/README.rst
doc/basic_usage.rst
doc/conf.py
doc/cutoff.rst
doc/index.rst
doc/logo.png
doc/make.bat
doc/method.rst
doc/predictive_capability_columns.rst
doc/rna_tools.rst
doc/small_dataset.rst
doc/_static/.gitkeep
doc/_templates/.gitkeep
doc/images/ct_3p.png
doc/images/dist_MCC.png
doc/images/dist_bw.png
doc/images/eFPR.png
doc/images/method.png
doc/images/profile.png
doc/images/profile_readcounts.png
doc/images/qc.png
doc/images/qc_overfit.png
doc/images/volcano.png
doc/images/volcano_threshold.png
epcy/__init__.py
epcy/__main__.py
epcy/epcy.py
epcy.egg-info/PKG-INFO
epcy.egg-info/SOURCES.txt
epcy.egg-info/dependency_links.txt
epcy.egg-info/entry_points.txt
epcy.egg-info/requires.txt
epcy.egg-info/top_level.txt
epcy/argparser/__init__.py
epcy/argparser/common.py
epcy/argparser/ct.py
epcy/argparser/explore.py
epcy/argparser/get_bandwidth_part.py
epcy/argparser/get_bootstrap_part.py
epcy/argparser/get_common_pred.py
epcy/argparser/get_common_profile.py
epcy/argparser/get_design_part.py
epcy/argparser/get_filter_part.py
epcy/argparser/get_gene_part.py
epcy/argparser/get_kallisto_part.py
epcy/argparser/get_log_part.py
epcy/argparser/get_matrix_part.py
epcy/argparser/get_output_part.py
epcy/argparser/get_rna_norm_part.py
epcy/argparser/kal2mat.py
epcy/argparser/pred.py
epcy/argparser/pred_rna.py
epcy/argparser/profile.py
epcy/argparser/profile_rna.py
epcy/argparser/qc.py
epcy/tests/__init__.py
epcy/tests/test.py
epcy/tools/__init__.py
epcy/tools/ct.py
epcy/tools/explore.py
epcy/tools/kal2mat.py
epcy/tools/pred.py
epcy/tools/pred_rna.py
epcy/tools/profile.py
epcy/tools/profile_rna.py
epcy/tools/qc.py
epcy/utils/Classifier.py
epcy/utils/__init__.py
epcy/utils/other.py
epcy/utils/plot.py
epcy/utils/readers.py