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Artemis
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2025-11-25 00:28:51 +08:00 |
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Monarch_util
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2025-11-25 00:28:51 +08:00 |
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PerlLib
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2025-11-25 00:28:51 +08:00 |
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TEST_SUPPORT/BFLY_TESTING
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alt_GG_read_partitioning_JCornish
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altsplice_simulation_toolkit
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bam_gene_tests
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blat_util
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insilico_norm_kmer_hists
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iso_reco_analysis
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sim_test_framework
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splice_path_analysis
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ButterflyFastaToGraphDot.pl
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2025-11-25 00:28:51 +08:00 |
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HiCpipe_nameSortedSam_to_raw.pl
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2025-11-25 00:28:51 +08:00 |
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Monarch
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N50.pl
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SAM_coordsorted_max_reads_per_position.pl
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SAM_intron_extractor.pl
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SAM_nameSorted_to_uniq_count_stats.pl
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SAM_pair_to_bed.pl
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SAM_show_alignment.pl
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SAM_show_alignment.summarize_stats.pl
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SAM_sortAny_to_count_stats.pl
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SAM_toString.pl
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SAM_to_bed.pl
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SAM_to_fasta.pl
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SAM_to_gff3.minimap2.pl
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SRA_to_fastq.notes
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SRA_to_fastq.pl
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STAR_align_log_parser.py
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TPM_weighted_gene_length.py
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TophatCufflinksWrapper.pl
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Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
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Trinity_node_seq_extractor.pl
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acc_list_to_fasta_entries.pl
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alexie_analyze_blast.pl
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align_reads_launch_igv.pl
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allele_simulator.pl
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analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
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analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
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analyze_blastPlus_topHit_coverage.extract_OS.pl
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analyze_blastPlus_topHit_coverage.org_matrix.pl
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average.pl
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blast_outfmt6_group_segments.pl
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blast_outfmt6_group_segments.to_Markov_Clustering.pl
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blast_outfmt6_group_segments.tophit_coverage.pl
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blastn_wrapper.pl
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capture_orig_n_unmapped_reads.pl
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cat_require_newlines.pl
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cdhit_examine_isoforms.pl
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cdna_fasta_file_to_transcript_gtf.pl
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check_chrysalis_graph_reciprocal_edges.pl
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check_fastQ_pair_ordering.pl
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chrys_graph_to_dot.pl
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collate_fqs.pl
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combined_nameSorted_to_dup_pairs_removed.pl
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compare_FL_stats.pl
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compare_bflies.pl
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component_to_graph_dot.pl
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contig_ExN50_statistic.pl
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convert_fasta_identifiers_for_FL_analysis.pl
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count_N50_given_MIN_FPKM_threshold.pl
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count_features_given_MIN_FPKM_threshold.pl
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count_iso_per_gene_dist.pl
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count_matrix_features_given_MIN_TPM_threshold.pl
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count_number_fasta_seqs.pl
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count_trans_per_component.pl
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decode_SAM_flag_value.pl
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describe_SAM_read_flag_info.pl
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determine_RF_strand_specificity.pl
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ensure_paired_end_bam_file.pl
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examine_iworm_FL_across_threads.pl
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2025-11-25 00:28:51 +08:00 |
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examine_strand_specificity.pl
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2025-11-25 00:28:51 +08:00 |
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examine_weldmer_halves.pl
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2025-11-25 00:28:51 +08:00 |
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extract_fastQ_pairings.pl
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2025-11-25 00:28:51 +08:00 |
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fan_out_fasta_seqs_to_indiv_files.pl
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2025-11-25 00:28:51 +08:00 |
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fastQ_append_acc.pl
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2025-11-25 00:28:51 +08:00 |
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fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
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2025-11-25 00:28:51 +08:00 |
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fastQ_rand_subset.pl
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fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
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fastQ_top_N_records.pl
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fasta_file_reformatter.pl
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fasta_filter_by_min_length.pl
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fasta_remove_duplicates.pl
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2025-11-25 00:28:51 +08:00 |
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fasta_seq_length.pl
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fasta_to_cmd_generator.pl
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2025-11-25 00:28:51 +08:00 |
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fasta_to_tab.pl
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fasta_write_sense_n_anti.pl
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fastq_cleaner.pl
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fastq_interleave_pairs.pl
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fastq_merge_sorted_tab_lists.pl
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fastq_stats.pl
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fastq_unweave_pairs.pl
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filter_out_accs_from_fasta.pl
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2025-11-25 00:28:51 +08:00 |
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filter_similar_seqs_expr_and_strand_aware.pl
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2025-11-25 00:28:51 +08:00 |
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flattened_gff_n_genome_to_Trinity_emulator.pl
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frag_boundary_to_wig.pl
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2025-11-25 00:28:51 +08:00 |
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frag_to_bed.pl
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2025-11-25 00:28:51 +08:00 |
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gene_gff3_to_introns.pl
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2025-11-25 00:28:51 +08:00 |
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gene_to_shared_transcript_content.pl
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2025-11-25 00:28:51 +08:00 |
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genome_gff3_to_gene_gff3_partitions.pl
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2025-11-25 00:28:51 +08:00 |
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get_GC_content_dist.pl
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2025-11-25 00:28:51 +08:00 |
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get_longest_isoform_seq_per_trinity_gene.pl
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get_path_nodes_from_fasta.pl
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get_welds_from_chrysals_graphFromFasta_out.pl
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gff3_file_to_cdna.pl
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gff3_file_utr_coverage_trimmer.pl
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gff3_to_genome_feature_base_encoding.parse_SAM.pl
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gff3_to_genome_feature_base_encoding.pl
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2025-11-25 00:28:51 +08:00 |
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gmap_gff3_chimera_jaccard_analyzer.pl
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gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
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2025-11-25 00:28:51 +08:00 |
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gmap_gff3_to_percent_length_stats.pl
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gmap_native_to_format_converter.pl
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gtf_to_bed_format.pl
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gtf_to_introns.pl
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hicpipe_raw_converter.pl
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identify_distal_isoform_variations.pl
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illustrate_ref_comparison.pl
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iworm_welds_to_dot.pl
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jaccard_sam_pair_refiner.pl
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join_any.pl
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join_by_left_col.pl
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join_expr_vals_single_table.pl
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kmer_counter.pl
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2025-11-25 00:28:51 +08:00 |
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m8_blastclust.pl
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map_gtf_transcripts_to_genome_annots.pl
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merge_RSEM_output_to_matrix.pl
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merge_blast_n_rsem_results.pl
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merge_replicate_bams_via_samples_file.pl
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merge_rsem_n_express_for_compare.pl
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mpi_iworm_proc_contigs_to_fa.pl
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nameSorted_SAM_to_FastQ.pl
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nameSorted_SAM_to_paired_fastq.pl
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omp_iworm_thread_contigs_to_fa.pl
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organize_data_table_by_trinity_component.pl
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pair_up_fastq_files_1_2.pl
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2025-11-25 00:28:51 +08:00 |
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pair_up_fastq_files_LeftRight.pl
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pair_up_fastq_files_R1_R2.pl
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pairwise_kmer_content_comparer.pl
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2025-11-25 00:28:51 +08:00 |
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plot_ExN50_statistic.Rscript
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plot_expressed_gene_dist.pl
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plot_strand_specificity_dist_by_quantile.Rscript
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print.pl
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print_kmers.pl
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process_GMAP_alignments_gff3_chimeras_ok.pl
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process_minimap2_alignments.pl
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prop_pair_sam_refiner.pl
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randomly_mutate_seqs.pl
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randomly_sample_PE_fastq.pl
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remove_cntrl_chars.pl
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rename_fasta_accessions_using_Trinotate_annot_mappings.pl
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row_to_column.pl
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run_DETONATE.pl
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run_GSNAP.pl
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run_HISAT.pl
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run_HISAT2_via_samples_file.pl
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run_HiCpipe_bowtie.pl
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run_STAR.pl
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run_STAR_via_samples_file.pl
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run_Stringtie_via_bam_file_list.pl
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run_TOPHAT.pl
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run_bowtie2.pl
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run_bwa.pl
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run_bwasw_trinity.pl
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run_jellyfish.pl
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run_read_simulator_per_fasta_entry.pl
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run_read_simulator_per_gene.pl
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run_trimmomatic_qual_trimming.pl
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seqinfo_refseq_to_dot.pl
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shuffle.pl
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simulate_illuminaPE_from_transcripts.pl
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simulate_illuminaPE_from_transcripts.wgsim.pl
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simulate_reads_sam_and_fa.pl
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sixFrameTranslation.pl
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sort_fastq.pl
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strip_fasta_header.pl
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tab_to_fastQ.pl
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tab_to_fasta.pl
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tblastn_wrapper.pl
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testUnlimitStacksize.pl
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transcript_coverage_UTR_trimmer.pl
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transcript_fasta_to_ORF_pics.pl
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transcript_gff3_to_bed.pl
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transdecoder_pep_to_false_fusion_finder.pl
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trinity_component_distribution.pl
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trinity_trans_matrix_to_rep_trans_gene_matrix.pl
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try_estimate_TPM_filtering_threshold.Rscript
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validate_fastqs.py
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