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trinityrnaseq 2.11.0%2Bdfsg-6
  • links: PTS, VCS
  • area: main
  • in suites: bullseye
  • size: 417,528 kB
  • sloc: perl: 48,420; cpp: 17,749; java: 12,695; python: 3,124; sh: 1,030; ansic: 983; makefile: 688; xml: 62

Folder: misc

d .. (parent)
d d rwxr-xr-x 52 Artemis
d d rwxr-xr-x 92 Monarch_util
d d rwxr-xr-x 36 PerlLib
d d rwxr-xr-x 33 TEST_SUPPORT
d d rwxr-xr-x 51 alt_GG_read_partitioning_JCornish
d d rwxr-xr-x 41 altsplice_simulation_toolkit
d d rwxr-xr-x 4,096 bam_gene_tests
d d rwxr-xr-x 4,096 blat_util
d d rwxr-xr-x 119 insilico_norm_kmer_hists
d d rwxr-xr-x 4,096 iso_reco_analysis
d d rwxr-xr-x 4,096 sim_test_framework
d d rwxr-xr-x 4,096 splice_path_analysis
- - rwxr-xr-x 1,693 ButterflyFastaToGraphDot.pl
- - rwxr-xr-x 2,289 HiCpipe_nameSortedSam_to_raw.pl
- - rwxr-xr-x 8,804 Monarch
- - rwxr-xr-x 881 N50.pl
- - rwxr-xr-x 1,035 SAM_coordsorted_max_reads_per_position.pl
- - rwxr-xr-x 3,570 SAM_intron_extractor.pl
- - rwxr-xr-x 7,681 SAM_nameSorted_to_uniq_count_stats.pl
- - rwxr-xr-x 1,965 SAM_pair_to_bed.pl
- - rwxr-xr-x 7,555 SAM_show_alignment.pl
- - rwxr-xr-x 4,142 SAM_show_alignment.summarize_stats.pl
- - rwxr-xr-x 4,415 SAM_sortAny_to_count_stats.pl
- - rwxr-xr-x 1,016 SAM_toString.pl
- - rwxr-xr-x 1,460 SAM_to_bed.pl
- - rwxr-xr-x 686 SAM_to_fasta.pl
- - rw-r--r-- 77 SRA_to_fastq.notes
- - rwxr-xr-x 1,655 SRA_to_fastq.pl
- - rwxr-xr-x 4,753 TPM_weighted_gene_length.py
- - rwxr-xr-x 4,884 TophatCufflinksWrapper.pl
- - rwxr-xr-x 9,621 Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
- - rwxr-xr-x 4,609 acc_list_to_fasta_entries.pl
- - rwxr-xr-x 36,122 alexie_analyze_blast.pl
- - rwxr-xr-x 1,260 align_reads_launch_igv.pl
- - rwxr-xr-x 2,180 allele_simulator.pl
- - rwxr-xr-x 2,676 analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
- - rwxr-xr-x 6,009 analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
- - rwxr-xr-x 2,158 analyze_blastPlus_topHit_coverage.extract_OS.pl
- - rwxr-xr-x 1,277 analyze_blastPlus_topHit_coverage.org_matrix.pl
- - rwxr-xr-x 790 average.pl
- - rwxr-xr-x 4,934 blast_outfmt6_group_segments.pl
- - rwxr-xr-x 4,432 blast_outfmt6_group_segments.to_Markov_Clustering.pl
- - rwxr-xr-x 3,033 blast_outfmt6_group_segments.tophit_coverage.pl
- - rwxr-xr-x 627 blastn_wrapper.pl
- - rw-r--r-- 5,593 capture_orig_n_unmapped_reads.pl
- - rwxr-xr-x 223 cat_require_newlines.pl
- - rwxr-xr-x 1,379 cdhit_examine_isoforms.pl
- - rwxr-xr-x 754 cdna_fasta_file_to_transcript_gtf.pl
- - rwxr-xr-x 1,008 check_chrysalis_graph_reciprocal_edges.pl
- - rwxr-xr-x 1,454 check_fastQ_pair_ordering.pl
- - rwxr-xr-x 492 chrys_graph_to_dot.pl
- - rwxr-xr-x 3,763 collate_fqs.pl
- - rwxr-xr-x 2,798 combined_nameSorted_to_dup_pairs_removed.pl
- - rwxr-xr-x 1,336 compare_FL_stats.pl
- - rwxr-xr-x 1,881 compare_bflies.pl
- - rwxr-xr-x 4,104 component_to_graph_dot.pl
- - rwxr-xr-x 4,089 contig_ExN50_statistic.pl
- - rwxr-xr-x 685 convert_fasta_identifiers_for_FL_analysis.pl
- - rwxr-xr-x 1,723 count_N50_given_MIN_FPKM_threshold.pl
- - rwxr-xr-x 769 count_features_given_MIN_FPKM_threshold.pl
- - rwxr-xr-x 668 count_iso_per_gene_dist.pl
- - rwxr-xr-x 877 count_matrix_features_given_MIN_TPM_threshold.pl
- - rwxr-xr-x 348 count_number_fasta_seqs.pl
- - rwxr-xr-x 1,090 count_trans_per_component.pl
- - rwxr-xr-x 1,662 decode_SAM_flag_value.pl
- - rwxr-xr-x 2,073 describe_SAM_read_flag_info.pl
- - rwxr-xr-x 2,477 determine_RF_strand_specificity.pl
- - rwxr-xr-x 922 ensure_paired_end_bam_file.pl
- - rwxr-xr-x 2,413 examine_iworm_FL_across_threads.pl
- - rwxr-xr-x 2,754 examine_strand_specificity.pl
- - rwxr-xr-x 2,307 examine_weldmer_halves.pl
- - rwxr-xr-x 6,608 extract_fastQ_pairings.pl
- - rwxr-xr-x 2,666 fan_out_fasta_seqs_to_indiv_files.pl
- - rwxr-xr-x 739 fastQ_append_acc.pl
- - rwxr-xr-x 2,459 fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
- - rwxr-xr-x 2,728 fastQ_rand_subset.pl
- - rwxr-xr-x 3,398 fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
- - rwxr-xr-x 644 fastQ_top_N_records.pl
- - rwxr-xr-x 450 fasta_file_reformatter.pl
- - rwxr-xr-x 544 fasta_filter_by_min_length.pl
- - rwxr-xr-x 679 fasta_remove_duplicates.pl
- - rwxr-xr-x 499 fasta_seq_length.pl
- - rwxr-xr-x 3,236 fasta_to_cmd_generator.pl
- - rwxr-xr-x 618 fasta_write_sense_n_anti.pl
- - rwxr-xr-x 1,578 fastq_cleaner.pl
- - rwxr-xr-x 1,297 fastq_interleave_pairs.pl
- - rwxr-xr-x 2,151 fastq_merge_sorted_tab_lists.pl
- - rwxr-xr-x 6,740 fastq_stats.pl
- - rwxr-xr-x 1,189 fastq_unweave_pairs.pl
- - rwxr-xr-x 1,127 filter_out_accs_from_fasta.pl
- - rwxr-xr-x 7,988 filter_similar_seqs_expr_and_strand_aware.pl
- - rwxr-xr-x 4,605 flattened_gff_n_genome_to_Trinity_emulator.pl
- - rwxr-xr-x 1,184 frag_boundary_to_wig.pl
- - rwxr-xr-x 470 frag_to_bed.pl
- - rwxr-xr-x 1,979 gene_gff3_to_introns.pl
- - rwxr-xr-x 1,998 gene_to_shared_transcript_content.pl
- - rwxr-xr-x 3,174 genome_gff3_to_gene_gff3_partitions.pl
- - rwxr-xr-x 1,518 get_GC_content_dist.pl
- - rwxr-xr-x 1,732 get_longest_isoform_seq_per_trinity_gene.pl
- - rwxr-xr-x 647 get_path_nodes_from_fasta.pl
- - rwxr-xr-x 391 get_welds_from_chrysals_graphFromFasta_out.pl
- - rwxr-xr-x 3,035 gff3_file_to_cdna.pl
- - rwxr-xr-x 6,881 gff3_file_utr_coverage_trimmer.pl
- - rwxr-xr-x 4,599 gff3_to_genome_feature_base_encoding.parse_SAM.pl
- - rwxr-xr-x 2,542 gff3_to_genome_feature_base_encoding.pl
- - rwxr-xr-x 4,814 gmap_gff3_chimera_jaccard_analyzer.pl
- - rwxr-xr-x 975 gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
- - rwxr-xr-x 1,856 gmap_gff3_to_percent_length_stats.pl
- - rwxr-xr-x 1,881 gmap_native_to_format_converter.pl
- - rwxr-xr-x 1,841 gtf_to_bed_format.pl
- - rwxr-xr-x 3,039 gtf_to_introns.pl
- - rwxr-xr-x 353 hicpipe_raw_converter.pl
- - rwxr-xr-x 4,732 identify_distal_isoform_variations.pl
- - rwxr-xr-x 4,816 illustrate_ref_comparison.pl
- - rwxr-xr-x 575 iworm_welds_to_dot.pl
- - rwxr-xr-x 2,751 jaccard_sam_pair_refiner.pl
- - rwxr-xr-x 828 join_any.pl
- - rwxr-xr-x 827 join_by_left_col.pl
- - rwxr-xr-x 929 join_expr_vals_single_table.pl
- - rwxr-xr-x 967 kmer_counter.pl
- - rwxr-xr-x 6,509 m8_blastclust.pl
- - rwxr-xr-x 16,748 map_gtf_transcripts_to_genome_annots.pl
- - rwxr-xr-x 3,088 merge_RSEM_output_to_matrix.pl
- - rwxr-xr-x 1,443 merge_blast_n_rsem_results.pl
- - rwxr-xr-x 1,904 merge_rsem_n_express_for_compare.pl
- - rwxr-xr-x 358 mpi_iworm_proc_contigs_to_fa.pl
- - rwxr-xr-x 1,724 nameSorted_SAM_to_FastQ.pl
- - rwxr-xr-x 4,034 nameSorted_SAM_to_paired_fastq.pl
- - rwxr-xr-x 556 omp_iworm_thread_contigs_to_fa.pl
- - rwxr-xr-x 439 organize_data_table_by_trinity_component.pl
- - rwxr-xr-x 491 pair_up_fastq_files_1_2.pl
- - rwxr-xr-x 584 pair_up_fastq_files_LeftRight.pl
- - rwxr-xr-x 606 pair_up_fastq_files_R1_R2.pl
- - rwxr-xr-x 1,780 pairwise_kmer_content_comparer.pl
- - rwxr-xr-x 783 plot_ExN50_statistic.Rscript
- - rwxr-xr-x 853 plot_expressed_gene_dist.pl
- - rwxr-xr-x 5,277 plot_strand_specificity_dist_by_quantile.Rscript
- - rwxr-xr-x 867 print.pl
- - rwxr-xr-x 626 print_kmers.pl
- - rwxr-xr-x 2,445 process_GMAP_alignments_gff3_chimeras_ok.pl
- - rwxr-xr-x 1,972 prop_pair_sam_refiner.pl
- - rwxr-xr-x 4,225 randomly_mutate_seqs.pl
- - rwxr-xr-x 3,120 randomly_sample_PE_fastq.pl
- - rwxr-xr-x 105 remove_cntrl_chars.pl
- - rwxr-xr-x 306 row_to_column.pl
- - rwxr-xr-x 2,308 run_DETONATE.pl
- - rwxr-xr-x 4,280 run_GSNAP.pl
- - rwxr-xr-x 4,876 run_HISAT.pl
- - rwxr-xr-x 4,016 run_HISAT2_via_samples_file.pl
- - rwxr-xr-x 1,207 run_HiCpipe_bowtie.pl
- - rwxr-xr-x 5,162 run_STAR.pl
- - rwxr-xr-x 5,681 run_STAR_via_samples_file.pl
- - rwxr-xr-x 1,845 run_TOPHAT.pl
- - rwxr-xr-x 1,864 run_bowtie2.pl
- - rwxr-xr-x 3,254 run_bwa.pl
- - rwxr-xr-x 1,160 run_bwasw_trinity.pl
- - rwxr-xr-x 1,393 run_jellyfish.pl
- - rwxr-xr-x 1,727 run_read_simulator_per_fasta_entry.pl
- - rwxr-xr-x 2,214 run_read_simulator_per_gene.pl
- - rwxr-xr-x 2,104 run_trimmomatic_qual_trimming.pl
- - rwxr-xr-x 4,191 seqinfo_refseq_to_dot.pl
- - rwxr-xr-x 212 shuffle.pl
- - rwxr-xr-x 9,322 simulate_illuminaPE_from_transcripts.pl
- - rwxr-xr-x 4,064 simulate_illuminaPE_from_transcripts.wgsim.pl
- - rwxr-xr-x 23,717 simulate_reads_sam_and_fa.pl
- - rwxr-xr-x 766 sixFrameTranslation.pl
- - rwxr-xr-x 1,176 sort_fastq.pl
- - rwxr-xr-x 428 strip_fasta_header.pl
- - rwxr-xr-x 282 tab_to_fastQ.pl
- - rwxr-xr-x 278 tab_to_fasta.pl
- - rwxr-xr-x 628 tblastn_wrapper.pl
- - rwxr-xr-x 1,798 testUnlimitStacksize.pl
- - rwxr-xr-x 4,617 transcript_coverage_UTR_trimmer.pl
- - rwxr-xr-x 5,811 transcript_fasta_to_ORF_pics.pl
- - rwxr-xr-x 1,990 transcript_gff3_to_bed.pl
- - rwxr-xr-x 1,500 transdecoder_pep_to_false_fusion_finder.pl
- - rwxr-xr-x 2,255 trinity_component_distribution.pl
- - rwxr-xr-x 1,726 trinity_trans_matrix_to_rep_trans_gene_matrix.pl