LICENSE
README.md
README.rst
pyproject.toml
setup.py
AltAnalyze3.egg-info/PKG-INFO
AltAnalyze3.egg-info/SOURCES.txt
AltAnalyze3.egg-info/dependency_links.txt
AltAnalyze3.egg-info/not-zip-safe
AltAnalyze3.egg-info/requires.txt
AltAnalyze3.egg-info/top_level.txt
altanalyze3/__init__.py
altanalyze3.egg-info/PKG-INFO
altanalyze3.egg-info/SOURCES.txt
altanalyze3.egg-info/dependency_links.txt
altanalyze3.egg-info/not-zip-safe
altanalyze3.egg-info/requires.txt
altanalyze3.egg-info/top_level.txt
altanalyze3/bin/__init__.py
altanalyze3/bin/altanalyze3
altanalyze3/components/__init__.py
altanalyze3/components/aggregate/__init__.py
altanalyze3/components/aggregate/main.py
altanalyze3/components/annotation/__init__.py
altanalyze3/components/annotation/ensembl_biomart.py
altanalyze3/components/annotation/junction_isoform.py
altanalyze3/components/gene_model/__init__.py
altanalyze3/components/gene_model/gene_model.py
altanalyze3/components/intron_count/__init__.py
altanalyze3/components/intron_count/main.py
altanalyze3/components/junction_count/__init__.py
altanalyze3/components/junction_count/main.py
altanalyze3/components/long_read/__init__.py
altanalyze3/components/long_read/comparisons.py
altanalyze3/components/long_read/gff_process.py
altanalyze3/components/long_read/isoform_automate.py
altanalyze3/components/long_read/isoform_junctions.py
altanalyze3/components/long_read/isoform_junctions_chunk.py
altanalyze3/components/long_read/isoform_matrix.py
altanalyze3/components/long_read/isoform_ratios.py
altanalyze3/components/long_read/isoform_snv.py
altanalyze3/components/long_read/isoform_translation.py
altanalyze3/components/oncosplice/PCAbasedFeatureSelection.py
altanalyze3/components/oncosplice/RoundWrapper.py
altanalyze3/components/oncosplice/__init__.py
altanalyze3/components/oncosplice/correlationDepletion.py
altanalyze3/components/oncosplice/determineNMFRank.py
altanalyze3/components/oncosplice/linearSVM.py
altanalyze3/components/oncosplice/main.py
altanalyze3/components/oncosplice/medianImpute.py
altanalyze3/components/oncosplice/metadataAnalysis.py
altanalyze3/components/oncosplice/preprocess.py
altanalyze3/components/oncosplice/removeRedundantSplicingEvents.py
altanalyze3/components/oncosplice/runNMF.py
altanalyze3/components/oncosplice/visualizations.py
altanalyze3/components/psi/__init__.py
altanalyze3/components/psi/main.py
altanalyze3/components/psi/main_backup.py
altanalyze3/components/psi/psi_single.py
altanalyze3/components/sparse/sparsify.py
altanalyze3/components/tests/BM_aging_MDS.py
altanalyze3/components/tests/BM_automated.py
altanalyze3/components/tests/JointProcessingScript.py
altanalyze3/components/tests/Ovarian.py
altanalyze3/components/udon/classificationFunctions.py
altanalyze3/components/udon/clustering_wrapper.py
altanalyze3/components/udon/determine_controls.py
altanalyze3/components/udon/enrichment_pathwaycommons.py
altanalyze3/components/udon/feature_selection.py
altanalyze3/components/udon/linearSVM.py
altanalyze3/components/udon/markerFinder.py
altanalyze3/components/udon/nmf.py
altanalyze3/components/udon/pre_process.py
altanalyze3/components/udon/visualizations.py
altanalyze3/utilities/__init__.py
altanalyze3/utilities/constants.py
altanalyze3/utilities/helpers.py
altanalyze3/utilities/io.py
altanalyze3/utilities/logger.py
altanalyze3/utilities/parser.py
doc/conf.py
docs/conf.py
tests/unit_tests/__init__.py
tests/unit_tests/test_data.py
tests/unit_tests/test_helpers.py
tests/unit_tests/test_intron_count.py
tests/unit_tests/test_io.py
tests/unit_tests/test_junction_count.py
tests/unit_tests/test_parser.py