MANIFEST.in
README.md
setup.py
PolTools/__init__.py
PolTools/cli.py
PolTools.egg-info/PKG-INFO
PolTools.egg-info/SOURCES.txt
PolTools.egg-info/dependency_links.txt
PolTools.egg-info/entry_points.txt
PolTools.egg-info/requires.txt
PolTools.egg-info/top_level.txt
PolTools/main_programs/TES_fold_change_heatmap.py
PolTools/main_programs/TES_heatmap.py
PolTools/main_programs/__init__.py
PolTools/main_programs/base_distribution.py
PolTools/main_programs/bigwigs_to_track_hubs.py
PolTools/main_programs/divergent_pileup_metaplot.py
PolTools/main_programs/gene_body_fold_change_heatmap.py
PolTools/main_programs/gene_body_heatmap.py
PolTools/main_programs/make_regions_file_centered_on_max_tss.py
PolTools/main_programs/metaplot.py
PolTools/main_programs/multicoverage.py
PolTools/main_programs/nucleotide_heatmap.py
PolTools/main_programs/pausing_distance_distribution_from_maxTSS.py
PolTools/main_programs/quantify_TES_fold_change_heatmap.py
PolTools/main_programs/quantify_gene_body_fold_change_heatmap.py
PolTools/main_programs/read_through_transcription.py
PolTools/main_programs/region_fold_change_heatmap.py
PolTools/main_programs/region_heatmap.py
PolTools/main_programs/sequence_from_region_around_max_tss.py
PolTools/main_programs/sequence_searches.py
PolTools/main_programs/tps_distance_per_gene.py
PolTools/main_programs/track_links_from_bw.py
PolTools/main_programs/truQuant.py
PolTools/main_programs/tsrFinder.py
PolTools/other_programs/RNA_Seq_align_and_quantify.py
PolTools/other_programs/TBP_dependent_tss_finder.py
PolTools/other_programs/__init__.py
PolTools/other_programs/add_bw_files.py
PolTools/other_programs/all_tss.py
PolTools/other_programs/counts_per_chromosome.py
PolTools/other_programs/frag_length_in_regions.py
PolTools/other_programs/histogram.py
PolTools/other_programs/make_big_ass_table.py
PolTools/other_programs/min_tracks.py
PolTools/other_programs/motif_distance_heatmap.py
PolTools/other_programs/motif_location.py
PolTools/other_programs/motif_location_heatmap.py
PolTools/other_programs/motif_location_heatmap_v2.py
PolTools/other_programs/nt_composition_in_long_genes.py
PolTools/other_programs/nt_sort_combine_gene_body_heatmap.py
PolTools/other_programs/nt_sort_fold_change_gene_body_heatmaps.py
PolTools/other_programs/nt_sort_gene_body_heatmap.py
PolTools/other_programs/polyAToPolyN.py
PolTools/other_programs/rolling_average_bigwigs.py
PolTools/other_programs/sorted_frag_length.py
PolTools/other_programs/truPeakFinder.py
PolTools/other_programs/tsr_picker.py
PolTools/static/hg38.GencodeV27.miRNA-rRNA-scRNA-snRNA-snoRNA-rRNA-scaRNA-tRNA.padded50bp.lsu_ssu.bed
PolTools/static/hg38.chrom.sizes.GC
PolTools/static/hg38.chrom.sizes.random
PolTools/static/longest_transcript_with_downstream_start_codon.txt
PolTools/utils/__init__.py
PolTools/utils/build_counts_dict.py
PolTools/utils/check_dependencies.py
PolTools/utils/constants.py
PolTools/utils/generate_blacklist_regions_for_gene_body_heatmap.py
PolTools/utils/get_region_length.py
PolTools/utils/make_random_filename.py
PolTools/utils/make_read_end_file.py
PolTools/utils/make_transcripts_dict.py
PolTools/utils/nested_multiprocessing_pool.py
PolTools/utils/print_tab_delimited.py
PolTools/utils/remove_files.py
PolTools/utils/tsrFinder
PolTools/utils/tsrFinder.cpp
PolTools/utils/tsr_finder_step_four_from_rocky.py
PolTools/utils/verify_bed_file.py
PolTools/utils/verify_region_length_is_even.py
PolTools/utils/bedtools_utils/__init__.py
PolTools/utils/bedtools_utils/run_bedtools_coverage.py
PolTools/utils/bedtools_utils/run_bedtools_getfasta.py
PolTools/utils/bedtools_utils/run_bedtools_subtract.py
PolTools/utils/heatmap_utils/__init__.py
PolTools/utils/heatmap_utils/add_matrices.py
PolTools/utils/heatmap_utils/average_matrix.py
PolTools/utils/heatmap_utils/generate_heatmap.R
PolTools/utils/heatmap_utils/generate_heatmap.py
PolTools/utils/heatmap_utils/get_max_value_from_matrix.py
PolTools/utils/heatmap_utils/get_min_value_from_matrix.py
PolTools/utils/heatmap_utils/make_log_two_fold_change_matrix.py
PolTools/utils/heatmap_utils/scale_matrix.py
PolTools/utils/heatmap_utils/set_matrix_bounds.py