LICENSE
MANIFEST.in
README.md
VERSION
changelog.md
isoquant.py
isoquant_detect_barcodes.py
isoquant_visualize.py
pyproject.toml
requirements.txt
requirements_tests.txt
isoquant.egg-info/PKG-INFO
isoquant.egg-info/SOURCES.txt
isoquant.egg-info/dependency_links.txt
isoquant.egg-info/entry_points.txt
isoquant.egg-info/requires.txt
isoquant.egg-info/top_level.txt
isoquant_lib/__init__.py
isoquant_lib/common.py
isoquant_lib/dataset_processor.py
isoquant_lib/gene_info.py
isoquant_lib/gtf2db.py
isoquant_lib/modes.py
isoquant_lib/parallel_workers.py
isoquant_lib/processed_read_manager.py
isoquant_lib/alignment/__init__.py
isoquant_lib/alignment/alignment_info.py
isoquant_lib/alignment/alignment_processor.py
isoquant_lib/assignment/__init__.py
isoquant_lib/assignment/assignment_aggregator.py
isoquant_lib/assignment/assignment_io.py
isoquant_lib/assignment/assignment_loader.py
isoquant_lib/assignment/exon_corrector.py
isoquant_lib/assignment/illumina_exon_corrector.py
isoquant_lib/assignment/isoform_assignment.py
isoquant_lib/assignment/junction_comparator.py
isoquant_lib/assignment/long_read_assigner.py
isoquant_lib/assignment/long_read_profiles.py
isoquant_lib/assignment/multimap_resolver.py
isoquant_lib/assignment/read_groups.py
isoquant_lib/barcode_calling/__init__.py
isoquant_lib/barcode_calling/common.py
isoquant_lib/barcode_calling/detect_barcodes.py
isoquant_lib/barcode_calling/umi_filtering.py
isoquant_lib/barcode_calling/callers/__init__.py
isoquant_lib/barcode_calling/callers/base.py
isoquant_lib/barcode_calling/callers/curio.py
isoquant_lib/barcode_calling/callers/extraction_result.py
isoquant_lib/barcode_calling/callers/molecule_structure.py
isoquant_lib/barcode_calling/callers/protocol.py
isoquant_lib/barcode_calling/callers/stereo.py
isoquant_lib/barcode_calling/callers/tenx.py
isoquant_lib/barcode_calling/callers/universal_extraction.py
isoquant_lib/barcode_calling/indexers/__init__.py
isoquant_lib/barcode_calling/indexers/base.py
isoquant_lib/barcode_calling/indexers/shared_memory.py
isoquant_lib/barcode_calling/indexers/two_bit.py
isoquant_lib/data/model_polya.json
isoquant_lib/data/model_polya_old.json
isoquant_lib/data/model_tss.json
isoquant_lib/data/model_tss_old.json
isoquant_lib/fusion/__init__.py
isoquant_lib/fusion/fusion_detector.py
isoquant_lib/fusion/fusion_metadata.py
isoquant_lib/fusion/fusion_validator.py
isoquant_lib/fusion/genomic_interval_index.py
isoquant_lib/model_construction/__init__.py
isoquant_lib/model_construction/assignment_based_constructor.py
isoquant_lib/model_construction/context.py
isoquant_lib/model_construction/end_processor.py
isoquant_lib/model_construction/fl_graph_constructor.py
isoquant_lib/model_construction/intron_graph.py
isoquant_lib/model_construction/intron_path.py
isoquant_lib/model_construction/model_construction.py
isoquant_lib/model_construction/model_filter.py
isoquant_lib/model_construction/model_read_counter.py
isoquant_lib/model_construction/read_assigner.py
isoquant_lib/model_construction/transcript_printer.py
isoquant_lib/model_construction/transcript_splice_site_corrector.py
isoquant_lib/model_construction/transcript_to_gene_joiner.py
isoquant_lib/quantification/__init__.py
isoquant_lib/quantification/convert_grouped_counts.py
isoquant_lib/quantification/long_read_counter.py
isoquant_lib/scripts/__init__.py
isoquant_lib/scripts/barcodes_seq_to_spot_id.py
isoquant_lib/scripts/convert_read_info.py
isoquant_lib/scripts/exon_splice_site_to_group_lists.py
isoquant_lib/scripts/inject_bam_tags.py
isoquant_lib/scripts/prepare_visium_spot_ids.py
isoquant_lib/terminal_prediction/__init__.py
isoquant_lib/terminal_prediction/cage_finder.py
isoquant_lib/terminal_prediction/polya_finder.py
isoquant_lib/terminal_prediction/polya_verification.py
isoquant_lib/terminal_prediction/terminal_counter.py
isoquant_lib/terminal_prediction/terminal_peaks.py
isoquant_lib/test_data/chr9.4M.fa.gz
isoquant_lib/test_data/chr9.4M.fa.gz.fai
isoquant_lib/test_data/chr9.4M.gtf.gz
isoquant_lib/test_data/chr9.4M.ont.sim.fq.gz
isoquant_lib/utils/__init__.py
isoquant_lib/utils/error_codes.py
isoquant_lib/utils/file_naming.py
isoquant_lib/utils/file_utils.py
isoquant_lib/utils/id_policy.py
isoquant_lib/utils/input_data_storage.py
isoquant_lib/utils/read_mapper.py
isoquant_lib/utils/serialization.py
isoquant_lib/utils/stats.py
isoquant_lib/utils/string_pools.py
isoquant_lib/utils/table_splitter.py
isoquant_lib/visualizer/__init__.py
isoquant_lib/visualizer/gene_model.py
isoquant_lib/visualizer/plot_output.py
isoquant_lib/visualizer/post_process.py
isoquant_lib/visualizer/process_dict.py