.gitignore
CHANGELOG.md
LICENSE
README.md
readthedocs.yml
setup.cfg
setup.py
docs/Makefile
docs/pybed-utils-notes.pdf
docs/requirements.txt
docs/source/api.rst
docs/source/cli.rst
docs/source/conf.py
docs/source/index.rst
docs/source/intro.rst
lifesci/__init__.py
lifesci/amino_acid_utils.py
lifesci/bam_utils.py
lifesci/bed_utils.py
lifesci/bio.py
lifesci/fastx_utils.py
lifesci/gene_ontology_utils.py
lifesci/gffread_utils.py
lifesci/gtf_utils.py
lifesci/igv.py
lifesci/meme_utils.py
lifesci/metacyc_utils.py
lifesci/mhcnames_utils.py
lifesci/mygene_utils.py
lifesci/pyensembl_utils.py
lifesci/sequence_similarity_utils.py
lifesci/star_utils.py
lifesci.egg-info/PKG-INFO
lifesci.egg-info/SOURCES.txt
lifesci.egg-info/dependency_links.txt
lifesci.egg-info/entry_points.txt
lifesci.egg-info/not-zip-safe
lifesci.egg-info/requires.txt
lifesci.egg-info/top_level.txt
lifesci/bio_programs/__init__.py
lifesci/bio_programs/bam_to_wiggle.py
lifesci/bio_programs/bed12_to_gtf.py
lifesci/bio_programs/bedx_to_bedy.py
lifesci/bio_programs/calculate_bed_overlap.py
lifesci/bio_programs/convert_ccds_to_bed.py
lifesci/bio_programs/count_aligned_reads.py
lifesci/bio_programs/count_reads.py
lifesci/bio_programs/create_mygene_report.py
lifesci/bio_programs/dna_to_aa.py
lifesci/bio_programs/download_srr_files.py
lifesci/bio_programs/extract_bed_sequences.py
lifesci/bio_programs/extract_cds_coordinates.py
lifesci/bio_programs/fasta_to_fastq.py
lifesci/bio_programs/fastq_pe_dedupe.py
lifesci/bio_programs/filter_bam_by_ids.py
lifesci/bio_programs/fix_all_bed_files.py
lifesci/bio_programs/get_all_utrs.py
lifesci/bio_programs/get_read_length_distribution.py
lifesci/bio_programs/gtf_to_bed12.py
lifesci/bio_programs/join_long_chromosomes.py
lifesci/bio_programs/merge_isoforms.py
lifesci/bio_programs/parse_meme_names.py
lifesci/bio_programs/remove_duplicate_bed_entries.py
lifesci/bio_programs/remove_duplicate_sequences.py
lifesci/bio_programs/remove_multimapping_reads.py
lifesci/bio_programs/reorder_fasta.py
lifesci/bio_programs/run_bowtie.py
lifesci/bio_programs/split_bed12_blocks.py
lifesci/bio_programs/split_long_chromosomes.py
lifesci/bio_programs/subtract_bed.py
lifesci/bio_programs/plotting/__init__.py
lifesci/bio_programs/plotting/create_aligned_read_count_bar_chart.py
lifesci/bio_programs/plotting/plot_read_length_distribution.py
tests/TestBedUtils.py
tests/TestGtfUtils.py
tests/__init__.py