site-packages/rectify/__init__.py
site-packages/rectify/__main__.py
site-packages/rectify/cli.py
site-packages/rectify/config.py
site-packages/rectify/core/__init__.py
site-packages/rectify/core/ag_mispriming.py
site-packages/rectify/core/aggregate_command.py
site-packages/rectify/core/align_command.py
site-packages/rectify/core/analyze/__init__.py
site-packages/rectify/core/analyze/apa_detection.py
site-packages/rectify/core/analyze/atract_refiner.py
site-packages/rectify/core/analyze/clustering.py
site-packages/rectify/core/analyze/deconvolution.py
site-packages/rectify/core/analyze/deseq2.py
site-packages/rectify/core/analyze/gene_attribution.py
site-packages/rectify/core/analyze/genomic_distribution.py
site-packages/rectify/core/analyze/go_enrichment.py
site-packages/rectify/core/analyze/heatmap.py
site-packages/rectify/core/analyze/junction_analysis.py
site-packages/rectify/core/analyze/junction_validation.py
site-packages/rectify/core/analyze/motif_discovery.py
site-packages/rectify/core/analyze/pan_mutant_refiner.py
site-packages/rectify/core/analyze/pca.py
site-packages/rectify/core/analyze/shift_analysis.py
site-packages/rectify/core/analyze/summary.py
site-packages/rectify/core/analyze_command.py
site-packages/rectify/core/atract_detector.py
site-packages/rectify/core/bam_processor.py
site-packages/rectify/core/batch_command.py
site-packages/rectify/core/chimeric_consensus.py
site-packages/rectify/core/consensus.py
site-packages/rectify/core/correct_command.py
site-packages/rectify/core/exclusion_regions.py
site-packages/rectify/core/export_command.py
site-packages/rectify/core/extract_command.py
site-packages/rectify/core/false_junction_filter.py
site-packages/rectify/core/indel_corrector.py
site-packages/rectify/core/junction_validator.py
site-packages/rectify/core/mpb_split_reads.py
site-packages/rectify/core/multi_aligner.py
site-packages/rectify/core/netseq_bam_processor.py
site-packages/rectify/core/netseq_command.py
site-packages/rectify/core/netseq_deconvolution.py
site-packages/rectify/core/netseq_output.py
site-packages/rectify/core/netseq_refiner.py
site-packages/rectify/core/polya_model.py
site-packages/rectify/core/polya_trimmer.py
site-packages/rectify/core/preprocess.py
site-packages/rectify/core/processing_stats.py
site-packages/rectify/core/run_command.py
site-packages/rectify/core/spikein_filter.py
site-packages/rectify/core/splice_aware_5prime.py
site-packages/rectify/core/terminal_exon_refiner.py
site-packages/rectify/core/test_command.py
site-packages/rectify/core/train_polya_command.py
site-packages/rectify/core/unified_record.py
site-packages/rectify/core/validate_command.py
site-packages/rectify/data/VALIDATION_READS.md
site-packages/rectify/data/__init__.py
site-packages/rectify/data/aligners/deSALT.bam
site-packages/rectify/data/aligners/deSALT.bam.bai
site-packages/rectify/data/aligners/gapmm2.bam
site-packages/rectify/data/aligners/gapmm2.bam.bai
site-packages/rectify/data/aligners/mapPacBio.bam
site-packages/rectify/data/aligners/mapPacBio.bam.bai
site-packages/rectify/data/aligners/minimap2.bam
site-packages/rectify/data/aligners/minimap2.bam.bai
site-packages/rectify/data/aligners/uLTRA.bam
site-packages/rectify/data/aligners/uLTRA.bam.bai
site-packages/rectify/data/gapmm2.bam
site-packages/rectify/data/gapmm2.bam.bai
site-packages/rectify/data/genomes/saccharomyces_cerevisiae/S288C_reference_sequence_R64-5-1_20240529.fsa.gz
site-packages/rectify/data/genomes/saccharomyces_cerevisiae/S288C_reference_sequence_R64-5-1_20240529.fsa.ncbi.gz
site-packages/rectify/data/genomes/saccharomyces_cerevisiae/bbmap_index/ref/genome/1/chr1.chrom.gz
site-packages/rectify/data/genomes/saccharomyces_cerevisiae/bbmap_index/ref/genome/1/scaffolds.txt.gz
site-packages/rectify/data/genomes/saccharomyces_cerevisiae/bbmap_index/ref/index/1/chr1_index_k12_c7_b1.block2.gz
site-packages/rectify/data/genomes/saccharomyces_cerevisiae/go_annotations.tsv.gz
site-packages/rectify/data/genomes/saccharomyces_cerevisiae/saccharomyces_cerevisiae_R64-5-1_20240529.gff.gz
site-packages/rectify/data/mapPacBio.bam
site-packages/rectify/data/mapPacBio.bam.bai
site-packages/rectify/data/minimap2.bam
site-packages/rectify/data/minimap2.bam.bai
site-packages/rectify/data/motif_databases/scerevisiae_tf_motifs.meme
site-packages/rectify/data/rectified.bam
site-packages/rectify/data/rectified.bam.bai
site-packages/rectify/data/rectified_softclip.bam
site-packages/rectify/data/rectified_softclip.bam.bai
site-packages/rectify/data/saccharomyces_cerevisiae_atract_netseq.tsv.gz
site-packages/rectify/data/saccharomyces_cerevisiae_netseq_pan.tsv.gz
site-packages/rectify/data/saccharomyces_cerevisiae_netseq_wt.tsv.gz
site-packages/rectify/data/validation_reads.bam
site-packages/rectify/data/validation_reads.bam.bai
site-packages/rectify/data/validation_reads.fastq.gz
site-packages/rectify/provenance.py
site-packages/rectify/slurm.py
site-packages/rectify/utils/__init__.py
site-packages/rectify/utils/alignment.py
site-packages/rectify/utils/chromosome.py
site-packages/rectify/utils/genome.py
site-packages/rectify/utils/junction_bed.py
site-packages/rectify/utils/provenance.py
site-packages/rectify/utils/splice_motif.py
site-packages/rectify/utils/stats.py
site-packages/rectify/visualize/__init__.py
site-packages/rectify/visualize/config.py
site-packages/rectify/visualize/coverage.py
site-packages/rectify/visualize/figure_utils.py
site-packages/rectify/visualize/gene_track.py
site-packages/rectify/visualize/metagene.py
site-packages/rectify/visualize/metagene_loaders.py
site-packages/rectify/visualize/multi_track.py
site-packages/rectify/visualize/read_browser.py
site-packages/rectify/visualize/ridge.py
site-packages/rectify/visualize/vep_panels.py
site-packages/rectify_rna-2.7.8.dist-info/INSTALLER
site-packages/rectify_rna-2.7.8.dist-info/METADATA
site-packages/rectify_rna-2.7.8.dist-info/RECORD
site-packages/rectify_rna-2.7.8.dist-info/REQUESTED
site-packages/rectify_rna-2.7.8.dist-info/WHEEL
site-packages/rectify_rna-2.7.8.dist-info/direct_url.json
site-packages/rectify_rna-2.7.8.dist-info/entry_points.txt
site-packages/rectify_rna-2.7.8.dist-info/licenses/LICENSE
site-packages/rectify_rna-2.7.8.dist-info/top_level.txt
