LICENSE
README.md
pyproject.toml
rectify/__init__.py
rectify/__main__.py
rectify/cli.py
rectify/config.py
rectify/provenance.py
rectify/slurm.py
rectify/core/__init__.py
rectify/core/ag_mispriming.py
rectify/core/aggregate_command.py
rectify/core/align_command.py
rectify/core/analyze_command.py
rectify/core/atract_detector.py
rectify/core/bam_processor.py
rectify/core/batch_command.py
rectify/core/chimeric_consensus.py
rectify/core/consensus.py
rectify/core/correct_command.py
rectify/core/exclusion_regions.py
rectify/core/export_command.py
rectify/core/extract_command.py
rectify/core/false_junction_filter.py
rectify/core/indel_corrector.py
rectify/core/junction_validator.py
rectify/core/mpb_split_reads.py
rectify/core/multi_aligner.py
rectify/core/netseq_bam_processor.py
rectify/core/netseq_command.py
rectify/core/netseq_deconvolution.py
rectify/core/netseq_output.py
rectify/core/netseq_refiner.py
rectify/core/polya_model.py
rectify/core/polya_trimmer.py
rectify/core/preprocess.py
rectify/core/processing_stats.py
rectify/core/run_command.py
rectify/core/spikein_filter.py
rectify/core/splice_aware_5prime.py
rectify/core/terminal_exon_refiner.py
rectify/core/test_command.py
rectify/core/train_polya_command.py
rectify/core/unified_record.py
rectify/core/validate_command.py
rectify/core/analyze/__init__.py
rectify/core/analyze/apa_detection.py
rectify/core/analyze/atract_refiner.py
rectify/core/analyze/clustering.py
rectify/core/analyze/deconvolution.py
rectify/core/analyze/deseq2.py
rectify/core/analyze/gene_attribution.py
rectify/core/analyze/genomic_distribution.py
rectify/core/analyze/go_enrichment.py
rectify/core/analyze/heatmap.py
rectify/core/analyze/junction_analysis.py
rectify/core/analyze/junction_validation.py
rectify/core/analyze/motif_discovery.py
rectify/core/analyze/pan_mutant_refiner.py
rectify/core/analyze/pca.py
rectify/core/analyze/shift_analysis.py
rectify/core/analyze/summary.py
rectify/data/VALIDATION_READS.md
rectify/data/__init__.py
rectify/data/gapmm2.bam
rectify/data/gapmm2.bam.bai
rectify/data/mapPacBio.bam
rectify/data/mapPacBio.bam.bai
rectify/data/minimap2.bam
rectify/data/minimap2.bam.bai
rectify/data/rectified.bam
rectify/data/rectified.bam.bai
rectify/data/rectified_softclip.bam
rectify/data/rectified_softclip.bam.bai
rectify/data/saccharomyces_cerevisiae_atract_netseq.tsv.gz
rectify/data/saccharomyces_cerevisiae_netseq_pan.tsv.gz
rectify/data/saccharomyces_cerevisiae_netseq_wt.tsv.gz
rectify/data/validation_reads.bam
rectify/data/validation_reads.bam.bai
rectify/data/validation_reads.fastq.gz
rectify/data/aligners/deSALT.bam
rectify/data/aligners/deSALT.bam.bai
rectify/data/aligners/gapmm2.bam
rectify/data/aligners/gapmm2.bam.bai
rectify/data/aligners/mapPacBio.bam
rectify/data/aligners/mapPacBio.bam.bai
rectify/data/aligners/minimap2.bam
rectify/data/aligners/minimap2.bam.bai
rectify/data/aligners/uLTRA.bam
rectify/data/aligners/uLTRA.bam.bai
rectify/data/genomes/saccharomyces_cerevisiae/S288C_reference_sequence_R64-5-1_20240529.fsa.gz
rectify/data/genomes/saccharomyces_cerevisiae/S288C_reference_sequence_R64-5-1_20240529.fsa.ncbi.gz
rectify/data/genomes/saccharomyces_cerevisiae/go_annotations.tsv.gz
rectify/data/genomes/saccharomyces_cerevisiae/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz
rectify/data/genomes/saccharomyces_cerevisiae/bbmap_index/ref/genome/1/chr1.chrom.gz
rectify/data/genomes/saccharomyces_cerevisiae/bbmap_index/ref/genome/1/scaffolds.txt.gz
rectify/data/genomes/saccharomyces_cerevisiae/bbmap_index/ref/index/1/chr1_index_k12_c7_b1.block2.gz
rectify/data/motif_databases/scerevisiae_tf_motifs.meme
rectify/utils/__init__.py
rectify/utils/alignment.py
rectify/utils/chromosome.py
rectify/utils/genome.py
rectify/utils/junction_bed.py
rectify/utils/provenance.py
rectify/utils/splice_motif.py
rectify/utils/stats.py
rectify/visualize/__init__.py
rectify/visualize/config.py
rectify/visualize/coverage.py
rectify/visualize/figure_utils.py
rectify/visualize/gene_track.py
rectify/visualize/metagene.py
rectify/visualize/metagene_loaders.py
rectify/visualize/multi_track.py
rectify/visualize/read_browser.py
rectify/visualize/ridge.py
rectify/visualize/vep_panels.py
rectify_rna.egg-info/PKG-INFO
rectify_rna.egg-info/SOURCES.txt
rectify_rna.egg-info/dependency_links.txt
rectify_rna.egg-info/entry_points.txt
rectify_rna.egg-info/requires.txt
rectify_rna.egg-info/top_level.txt
tests/test_ag_mispriming.py
tests/test_analyze.py
tests/test_apa_detection.py
tests/test_atract.py
tests/test_chimeric_consensus.py
tests/test_config.py
tests/test_gapmm2_seq_restore.py
tests/test_indel_correction.py
tests/test_junction_validator.py
tests/test_metagene.py
tests/test_metagene_loaders.py
tests/test_netseq_refiner.py
tests/test_no_duplicate_primaries.py
tests/test_parallel_aligner_schedule.py
tests/test_parallel_processing.py
tests/test_polya_trimming.py
tests/test_provenance_and_spikein.py
tests/test_run_command_wiring.py
tests/test_sample_column_autodetect.py
tests/test_slurm.py
tests/test_splice_junction.py
tests/test_validation_reads.py
tests/test_variant_aware_rescue.py
tests/test_xr_flag.py