├── .gitignore ├── LICENSE ├── README.md ├── README.rst ├── bashrc ├── gitignore ├── oolite_bash_settings_current ├── screenrc └── tscc_bash_settings_current ├── bin └── make_project ├── gscripts ├── GO │ ├── GO.py │ └── __init__.py ├── __init__.py ├── annotations │ ├── __init__.py │ ├── gencode_annotate_utrs_5p_3p.pl │ └── miso.py ├── assembly │ ├── __init__.py │ └── align_reads.py ├── clipseq │ ├── __init__.py │ ├── add_randomer.py │ ├── barcode_collapse.py │ ├── barcode_collapse_pe.py │ ├── barcode_frequency.py │ ├── calculate_frip.py │ ├── clipseq_barcode_metrics.py │ ├── coverage_utils.py │ ├── cross_contamination_detector.py │ ├── demultiplex_barcoded_fastq.py │ ├── demux_paired_end.py │ ├── fix_scores.py │ ├── fold_change_from_l2_fold_change.py │ ├── kasey_peak_calling │ │ ├── allocate_reads_to_gene_hg19_fromBED.pl │ │ ├── allocate_reads_to_gene_mm9_fromBED.pl │ │ ├── allocate_reads_to_genes_hg19.pl │ │ ├── analyze_clip_data_complete │ │ ├── analyze_clip_data_complete_old │ │ ├── analyze_clip_data_complete_old2 │ │ ├── analyze_clip_data_complete_old3 │ │ ├── clip_pipeline_hg19.sh │ │ ├── clusterid_location_ce6 │ │ ├── clusterid_location_ce6.pre │ │ ├── clusterid_location_hg18 │ │ ├── clusterid_location_hg18.pre │ │ ├── clusterid_location_hg19 │ │ ├── clusterid_location_hg19.old │ │ ├── clusterid_location_hg19.pre │ │ ├── clusterid_location_hg19.pre.old │ │ ├── clusterid_location_mm8 │ │ ├── clusterid_location_mm8.pre │ │ ├── clusterid_location_mm9 │ │ ├── clusterid_location_mm9.pre │ │ ├── count_clusters │ │ ├── count_tags2ids │ │ ├── grouped_hg18_exp │ │ ├── junk_sorter │ │ ├── poisson_ingenes_vw3_ce6 │ │ ├── poisson_ingenes_vw3_hg18 │ │ ├── poisson_ingenes_vw3_hg19 │ │ ├── poisson_ingenes_vw3_mm8 │ │ ├── poisson_ingenes_vw3_mm8_2 │ │ ├── poisson_ingenes_vw3_mm9 │ │ ├── poisson_notingenes_vw3_hg18 │ │ ├── poisson_notingenes_vw3_hg19 │ │ ├── poisson_notingenes_vw3_mm8 │ │ ├── poisson_notingenes_vw3_mm9 │ │ ├── remove_repeats_hg18 │ │ ├── remove_repeats_mm8 │ │ ├── remove_repeats_mm9 │ │ ├── remove_user_repeats_hg18 │ │ ├── remove_user_repeats_mm8 │ │ ├── remove_user_repeats_mm9 │ │ ├── sort_clusters_bed_normalized_histo_mm8 │ │ ├── sort_clusters_bed_normalized_histo_mm9 │ │ ├── sort_clusters_bed_normalized_histo_subsetmm8 │ │ ├── sort_clusters_bed_normalized_histo_subsetmm9 │ │ ├── sort_clusters_general_normalized_histo_ce6 │ │ ├── sort_clusters_general_normalized_histo_hg18 │ │ ├── sort_clusters_general_normalized_histo_hg19 │ │ ├── sort_clusters_general_normalized_histo_mm8 │ │ ├── sort_clusters_general_normalized_histo_mm8_old │ │ ├── sort_clusters_general_normalized_histo_mm9 │ │ ├── sort_clusters_ingenes_normalized_histo_ce6 │ │ ├── sort_clusters_ingenes_normalized_histo_hg18 │ │ ├── sort_clusters_ingenes_normalized_histo_hg19 │ │ ├── sort_clusters_ingenes_normalized_histo_mm8 │ │ ├── sort_clusters_ingenes_normalized_histo_mm9 │ │ ├── sort_clusters_to_exons_hg18 │ │ ├── sort_tags_clip_notrim_ce6 │ │ ├── sort_tags_clip_notrim_hg18 │ │ ├── sort_tags_clip_notrim_hg19 │ │ ├── sort_tags_clip_notrim_mm8 │ │ ├── sort_tags_clip_notrim_mm9 │ │ ├── sort_tags_clip_trim_ce6 │ │ ├── sort_tags_clip_trim_hg18 │ │ ├── sort_tags_clip_trim_hg19 │ │ ├── sort_tags_clip_trim_mm8 │ │ ├── sort_tags_clip_trim_mm9 │ │ ├── sort_tags_ingenes_ce6 │ │ ├── sort_tags_ingenes_hg18 │ │ ├── sort_tags_ingenes_hg19 │ │ ├── sort_tags_ingenes_mm8 │ │ ├── sort_tags_ingenes_mm8_temp │ │ ├── sort_tags_ingenes_mm9 │ │ ├── sort_tags_notingenes_ce6 │ │ ├── sort_tags_notingenes_hg18 │ │ ├── sort_tags_notingenes_hg19 │ │ ├── sort_tags_notingenes_mm8 │ │ └── sort_tags_notingenes_mm9 │ ├── kmer_extractor.py │ ├── pe_barcode_splitter.py │ ├── perform_idr.py │ ├── remove_randomers.py │ ├── remove_softclip.py │ ├── run_kasey.py │ ├── run_piranha.py │ ├── run_ripseeker.R │ ├── run_ripseeker.py │ └── sort_fastq.py ├── command_line_template.py ├── conservation │ ├── README │ ├── __init__.py │ ├── download_conservation.sh │ ├── index_conservation.sh │ ├── maf_handler.py │ ├── maf_mucking.py │ └── maf_scorer.py ├── dexseq │ └── __init__.py ├── editing │ ├── __init__.py │ ├── create_rna_editing_makefile.py │ └── template.mk ├── encode │ └── encode_helpers.py ├── example_gitignore ├── expr_db │ ├── db_walker.py │ ├── record_fto.py │ ├── seq_db.py │ └── test_seqdb.py ├── general │ ├── __init__.py │ ├── _read_sample_info_file.py │ ├── add_in_extra_genes.py │ ├── analysis_tools.py │ ├── bamTobowtie.py │ ├── bigwig_corr.py │ ├── calculate_NRF.py │ ├── cat_biogem.py │ ├── cat_files.py │ ├── cat_rapidrun.py │ ├── count_aligned_from_bam.py │ ├── count_aligned_from_sam.py │ ├── covToVector.py │ ├── create_RPKM_table.pl │ ├── dataviz.py │ ├── downsample_bam.py │ ├── downsample_fastq.py │ ├── fastq_groupby_and_cat.py │ ├── filter_bam_read_length.py │ ├── gene_lists.py │ ├── group_files_by_extension.pl │ ├── gsnap_index.py │ ├── gtf2gff3.pl │ ├── intersection_helpers.py │ ├── logger.py │ ├── make_bigwig_entropy.py │ ├── make_bigwig_entropy_files.py │ ├── make_bigwig_files.py │ ├── make_bigwig_files_pe.py │ ├── make_links.pl │ ├── make_trackhubs.py │ ├── negBedGraph.py │ ├── normalize_bedGraph.py │ ├── parsers.py │ ├── pybedtools_helpers.py │ ├── region_helpers.py │ ├── spin.py │ ├── split_bam.py │ ├── submit_fastqc.py │ └── venn_matrix.py ├── ipython_imports.py ├── ipython_server │ └── serve_ipython.py ├── mapping │ ├── __init__.py │ ├── convert_sam.py │ ├── count_spikeins.sh │ ├── downsample.py │ ├── fastq_filters.py │ ├── genome_generate.py │ ├── index_bam.py │ ├── map_paired_or_single_with_STAR.py │ ├── map_paired_with_STAR.py~ │ ├── remove_spliced_reads.py │ ├── repeat_align.py │ ├── sam_to_bam_and_sort.py │ └── sort_bam.py ├── math │ └── __init__.py ├── mirna │ └── miR_splitter.py ├── miso │ ├── __init__.py │ ├── concatenate_miso.py │ ├── convert_ids.py │ ├── filter_miso.py │ ├── find_nan_miso_events.py │ ├── submit_concatenate_miso.py │ ├── submit_index_gff.py │ ├── submit_index_gff.sh~ │ ├── submit_index_gff_template.sh~ │ └── submit_miso_pipeline.py ├── modality │ ├── __init__.py │ └── exploration.py ├── output_parsers │ ├── __init__.py │ ├── parseMiso.py │ └── rna_star_collector.py ├── pwm │ ├── __init__.py │ ├── cisbp_template.txt │ └── cisbp_to_meme.py ├── qtools │ ├── _Submitter.py │ └── __init__.py ├── riboseq │ ├── HnRNPClustersToEns.sh │ ├── RBP_peak_density_genome.sh │ ├── RBP_peak_density_mRNA.sh │ ├── RiboSeqPeaksToEns.sh │ ├── __init__.py │ ├── ensMapper.py │ ├── ensMapper.sh │ ├── hg19ToEns.sh │ ├── randomized_mapping.sh │ ├── read_filter.py │ ├── remove_redundant_transcripts.py │ ├── riboseq_coverage.py │ ├── riboseq_mapper.sh │ ├── riboseq_peak_density_genome.sh │ ├── riboseq_peak_density_mRNA.sh │ ├── riboseq_peak_finder.py │ ├── riboseq_utils.py │ └── uorf_detector.py ├── rnaseq │ ├── __init__.py │ ├── count_bam.py │ ├── count_detected_oldsplice.py │ ├── count_reads_broadfeatures_frombamfi.pl │ ├── count_tags.py │ ├── count_whole_gene_sense.py │ ├── create_RPKM_table.pl │ ├── cufflinks.py │ ├── helpers.py │ ├── make_rnaseqc.py │ ├── oldsplice.py │ ├── oldsplice_gff.py │ ├── parse_oldsplice.py │ ├── rpkmZ.py │ ├── rpkm_from_counts.py │ ├── sailfish_index.py │ ├── sailfish_quant.py │ ├── single_RPKM.py │ ├── splicing_map.py │ ├── splicing_modality.py │ ├── submit_oldsplice.py │ ├── submit_oldsplice_gff.py │ ├── submit_parse_oldsplice.py │ ├── submit_rnaseqc.py │ └── submit_rseqc.sh ├── ssgsea │ ├── OPAM.library.v7.R │ └── ssgsea_example.R └── structure │ ├── __init__.py │ ├── conserved_structure.py │ ├── generate_scores.sh │ ├── generate_shuffled_regions.sh │ ├── get_regions.py │ ├── parseRNAhybrid.pl │ ├── rnafolds.py │ ├── runConsStruc1.sh │ ├── shuffle_bridges.py │ ├── shuffle_bridges.py~ │ ├── shuffle_bridges_small_input.py │ ├── shuffle_script.sh │ ├── shuffled_mfe.sh │ ├── split_bridges.py │ └── structure.py ├── out.sam ├── perl_scripts ├── Peak_input_normalization_wrapper.pl ├── compress_l2foldenrpeakfi.pl ├── overlap_peakfi_with_bam_PE.pl ├── overlap_peakfi_with_bam_PE_gabesstupidversion.pl └── overlap_peakfi_with_bam_PE_gabesstupidversion.pl~ ├── qscripts ├── #analyze_pip_seq.scala# ├── Aligned.out.sam ├── analyze_clip_seq.scala ├── analyze_clip_seq_encode.scala ├── analyze_clip_seq_encode.scala~ ├── analyze_clip_seq_encode_downsample.scala ├── analyze_clip_seq_encode_se.scala ├── analyze_clip_seq_encode_se_true.scala ├── analyze_clip_seq_from_bam.scala ├── analyze_clip_seq_from_bam.scala~ ├── analyze_downsample.scala ├── analyze_idr.scala ├── analyze_miRli.scala ├── analyze_pip_seq.scala ├── analyze_ribo_seq.scala ├── analyze_ribo_seq.scala~ ├── analyze_rna_seq.scala ├── analyze_rna_seq_from_bam.scala ├── analyze_rna_seq_from_bam.scala~ ├── analyze_rna_seq_from_bam_v2.scala ├── analyze_rna_seq_gently.scala ├── analyze_rna_seq_spikein.scala ├── expr_db │ ├── db_walker.py │ └── seq_db.py └── run_many_jobs.scala ├── setup.py ├── setuptools_git-1.0-py2.7.egg └── tests ├── __init__.py ├── data ├── barcode_test.fastq ├── gff_uorf_test.fa ├── gff_uorf_test.gff ├── rpkm_test.rpkm ├── sample_info.txt ├── test.bam ├── test.sam ├── test_barcode_collapse.bam ├── test_barcode_collapse.bam.bai ├── test_barcode_collapse.bc.bam ├── test_barcode_collapse.bc.bam.barcodes.wiggle ├── test_barcode_collapse.bc.bam.entropy.wiggle ├── test_barcode_collapse.bc.bam.total.wiggle ├── test_cross_contamination │ ├── grouped_files │ │ ├── duplicate_neg.bam │ │ ├── duplicate_neg.bam.bai │ │ ├── duplicate_pos.bam │ │ ├── duplicate_pos.bam.bai │ │ ├── pos_vs_neg.bam │ │ ├── pos_vs_neg.bam.bai │ │ ├── randomer_match_neg.bam │ │ ├── randomer_match_neg.bam.bai │ │ ├── randomer_match_neg2.bam │ │ ├── randomer_match_neg2.bam.bai │ │ ├── randomer_match_pos.bam │ │ ├── randomer_match_pos.bam.bai │ │ ├── randomer_mismatch_neg.bam │ │ ├── randomer_mismatch_neg.bam.bai │ │ ├── randomer_mismatch_pos.bam │ │ ├── randomer_mismatch_pos.bam.bai │ │ ├── randomer_off_by_one_neg.bam │ │ ├── randomer_off_by_one_neg.bam.bai │ │ ├── randomer_off_by_one_pos.bam │ │ └── randomer_off_by_one_pos.bam.bai │ ├── negative1.bam │ ├── negative1.bam.bai │ ├── negative2.bam │ ├── negative_duplicate.bam │ ├── negative_duplicate.bam.bai │ ├── negative_match.bam │ ├── negative_match.bam.bai │ ├── negative_mismatch.bam │ ├── negative_mismatch.bam.bai │ ├── negative_off_by_one.bam │ ├── negative_off_by_one.bam.bai │ ├── positive.bam │ ├── positive.bam.bai │ ├── positive1.bam │ ├── positive1.bam.bai │ ├── positive_duplicate.bam │ ├── positive_duplicate.bam.bai │ ├── positive_match.bam │ ├── positive_match.bam.bai │ ├── positive_mismatch.bam │ ├── positive_mismatch.bam.bai │ ├── positive_off_by_one.bam │ └── positive_off_by_one.bam.bai ├── test_qtools_submitter.sh ├── test_qtools_submitter_wait_for_pbs.sh └── test_single_RPKM.count ├── test_barcode_collapse.py ├── test_barcode_frequency.py ├── test_convert_sam.py ├── test_count_bam.py ├── test_count_tags.py ├── test_cross_contamination.py ├── test_cufflinks.py ├── 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