LICENSE
README.md
setup.cfg
setup.py
src/pbiotools/__init__.py
src/pbiotools.egg-info/PKG-INFO
src/pbiotools.egg-info/SOURCES.txt
src/pbiotools.egg-info/dependency_links.txt
src/pbiotools.egg-info/entry_points.txt
src/pbiotools.egg-info/not-zip-safe
src/pbiotools.egg-info/requires.txt
src/pbiotools.egg-info/top_level.txt
src/pbiotools/misc/__init__.py
src/pbiotools/misc/dask_utils.py
src/pbiotools/misc/latex.py
src/pbiotools/misc/logging_utils.py
src/pbiotools/misc/math_utils.py
src/pbiotools/misc/mpl_utils.py
src/pbiotools/misc/pandas_utils.py
src/pbiotools/misc/parallel.py
src/pbiotools/misc/shell_utils.py
src/pbiotools/misc/slurm.py
src/pbiotools/misc/suppress_stdout_stderr.py
src/pbiotools/misc/utils.py
src/pbiotools/misc/pgrms/__init__.py
src/pbiotools/misc/pgrms/pickle_stan.py
src/pbiotools/ribo/__init__.py
src/pbiotools/ribo/ribo_filenames.py
src/pbiotools/ribo/ribo_utils.py
src/pbiotools/ribo/pgrms/__init__.py
src/pbiotools/ribo/pgrms/estimate_metagene_profile_bayes_factors.py
src/pbiotools/ribo/pgrms/extract_metagene_profiles.py
src/pbiotools/ribo/pgrms/select_periodic_offsets.py
src/pbiotools/utils/__init__.py
src/pbiotools/utils/bam_utils.py
src/pbiotools/utils/bed_utils.py
src/pbiotools/utils/bio.py
src/pbiotools/utils/fastx_utils.py
src/pbiotools/utils/gffread_utils.py
src/pbiotools/utils/gtf_utils.py
src/pbiotools/utils/igv.py
src/pbiotools/utils/meme_utils.py
src/pbiotools/utils/metacyc_utils.py
src/pbiotools/utils/mygene_utils.py
src/pbiotools/utils/pgrm_utils.py
src/pbiotools/utils/pyensembl_utils.py
src/pbiotools/utils/pgrms/__init__.py
src/pbiotools/utils/pgrms/bam_to_wiggle.py
src/pbiotools/utils/pgrms/bed12_to_gtf.py
src/pbiotools/utils/pgrms/bed_to_bigBed.py
src/pbiotools/utils/pgrms/bedx_to_bedy.py
src/pbiotools/utils/pgrms/calculate_bed_overlap.py
src/pbiotools/utils/pgrms/convert_ccds_to_bed.py
src/pbiotools/utils/pgrms/count_aligned_reads.py
src/pbiotools/utils/pgrms/count_reads.py
src/pbiotools/utils/pgrms/create_init_ribo_track.py
src/pbiotools/utils/pgrms/create_mygene_report.py
src/pbiotools/utils/pgrms/dna_to_aa.py
src/pbiotools/utils/pgrms/download_srr_files.py
src/pbiotools/utils/pgrms/extract_bed_sequences.py
src/pbiotools/utils/pgrms/extract_cds_coordinates.py
src/pbiotools/utils/pgrms/fasta_to_fastq.py
src/pbiotools/utils/pgrms/fastq_pe_dedupe.py
src/pbiotools/utils/pgrms/filter_bam_by_ids.py
src/pbiotools/utils/pgrms/fix_all_bed_files.py
src/pbiotools/utils/pgrms/get_all_utrs.py
src/pbiotools/utils/pgrms/get_read_length_distribution.py
src/pbiotools/utils/pgrms/gtf_to_bed12.py
src/pbiotools/utils/pgrms/join_long_chromosomes.py
src/pbiotools/utils/pgrms/merge_isoforms.py
src/pbiotools/utils/pgrms/parse_meme_names.py
src/pbiotools/utils/pgrms/remove_duplicate_bed_entries.py
src/pbiotools/utils/pgrms/remove_duplicate_sequences.py
src/pbiotools/utils/pgrms/remove_multimapping_reads.py
src/pbiotools/utils/pgrms/reorder_fasta.py
src/pbiotools/utils/pgrms/run_bowtie.py
src/pbiotools/utils/pgrms/run_signalp.py
src/pbiotools/utils/pgrms/run_tmhmm.py
src/pbiotools/utils/pgrms/split_bed12_blocks.py
src/pbiotools/utils/pgrms/split_long_chromosomes.py
src/pbiotools/utils/pgrms/subtract_bed.py
src/pbiotools/utils/pgrms/plotsc/__init__.py
src/pbiotools/utils/pgrms/plotsc/create_aligned_read_count_bar_chart.py
src/pbiotools/utils/pgrms/plotsc/plot_read_length_distribution.py