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trinityrnaseq 2.2.0%2Bdfsg-2
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 212,452 kB
  • ctags: 5,067
  • sloc: perl: 45,552; cpp: 19,678; java: 11,865; sh: 1,485; makefile: 613; ansic: 427; python: 313; xml: 83

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 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 splice_path_analysis
- - rwxr-xr-x 21,363 BLAT_to_SAM.pl
- - rwxr-xr-x 1,708 ButterflyFastaToGraphDot.pl
- - rwxr-xr-x 2,304 HiCpipe_nameSortedSam_to_raw.pl
- - rwxr-xr-x 8,866 Monarch
- - rwxr-xr-x 895 N50.pl
- - rwxr-xr-x 1,049 SAM_coordsorted_max_reads_per_position.pl
- - rwxr-xr-x 3,584 SAM_intron_extractor.pl
- - rwxr-xr-x 1,979 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 4,429 SAM_sortAny_to_count_stats.pl
- - rwxr-xr-x 1,030 SAM_toString.pl
- - rwxr-xr-x 1,495 SAM_to_bed.pl
- - rwxr-xr-x 700 SAM_to_fasta.pl
- - rw-r--r-- 77 SRA_to_fastq.notes
- - rwxr-xr-x 1,655 SRA_to_fastq.pl
- - rwxr-xr-x 4,897 TophatCufflinksWrapper.pl
- - rwxr-xr-x 4,216 acc_list_to_fasta_entries.pl
- - rwxr-xr-x 36,122 alexie_analyze_blast.pl
- - rwxr-xr-x 2,194 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 804 average.pl
- - rwxr-xr-x 4,433 blast_outfmt6_group_segments.pl
- - rwxr-xr-x 4,446 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-- 5,607 capture_orig_n_unmapped_reads.pl
- - rwxr-xr-x 223 cat_require_newlines.pl
- - rwxr-xr-x 768 cdna_fasta_file_to_transcript_gtf.pl
- - rwxr-xr-x 1,382 check_fastQ_pair_ordering.pl
- - rwxr-xr-x 492 chrys_graph_to_dot.pl
- - rwxr-xr-x 2,798 combined_nameSorted_to_dup_pairs_removed.pl
- - rwxr-xr-x 1,918 compare_bflies.pl
- - rwxr-xr-x 4,104 component_to_graph_dot.pl
- - rwxr-xr-x 3,353 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 904 count_matrix_features_given_MIN_TPM_threshold.pl
- - rwxr-xr-x 348 count_number_fasta_seqs.pl
- - rwxr-xr-x 1,104 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 2,413 examine_iworm_FL_across_threads.pl
- - rwxr-xr-x 2,307 examine_weldmer_halves.pl
- - rwxr-xr-x 6,622 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 2,742 fastQ_rand_subset.pl
- - rwxr-xr-x 3,412 fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
- - rwxr-xr-x 644 fastQ_top_N_records.pl
- - rwxr-xr-x 464 fasta_file_reformatter.pl
- - rwxr-xr-x 558 fasta_filter_by_min_length.pl
- - rwxr-xr-x 679 fasta_remove_duplicates.pl
- - rwxr-xr-x 508 fasta_seq_length.pl
- - rwxr-xr-x 3,250 fasta_to_cmd_generator.pl
- - rwxr-xr-x 632 fasta_write_sense_n_anti.pl
- - rwxr-xr-x 1,578 fastq_cleaner.pl
- - rwxr-xr-x 1,311 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 1,203 fastq_unweave_pairs.pl
- - rwxr-xr-x 1,184 frag_boundary_to_wig.pl
- - rwxr-xr-x 483 frag_to_bed.pl
- - rwxr-xr-x 1,993 gene_gff3_to_introns.pl
- - rwxr-xr-x 1,998 gene_to_shared_transcript_content.pl
- - rwxr-xr-x 3,187 genome_gff3_to_gene_gff3_partitions.pl
- - rwxr-xr-x 1,746 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 3,049 gff3_file_to_cdna.pl
- - rwxr-xr-x 6,895 gff3_file_utr_coverage_trimmer.pl
- - rwxr-xr-x 4,613 gff3_to_genome_feature_base_encoding.parse_SAM.pl
- - rwxr-xr-x 2,556 gff3_to_genome_feature_base_encoding.pl
- - rwxr-xr-x 4,828 gmap_gff3_chimera_jaccard_analyzer.pl
- - rwxr-xr-x 975 gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
- - rwxr-xr-x 1,870 gmap_gff3_to_percent_length_stats.pl
- - rwxr-xr-x 1,895 gmap_native_to_format_converter.pl
- - rwxr-xr-x 1,855 gtf_to_bed_format.pl
- - rwxr-xr-x 3,053 gtf_to_introns.pl
- - rwxr-xr-x 353 hicpipe_raw_converter.pl
- - rwxr-xr-x 4,741 identify_distal_isoform_variations.pl
- - rwxr-xr-x 4,633 illustrate_ref_comparison.pl
- - rwxr-xr-x 2,765 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 981 kmer_counter.pl
- - rwxr-xr-x 6,523 m8_blastclust.pl
- - rwxr-xr-x 16,762 map_gtf_transcripts_to_genome_annots.pl
- - rwxr-xr-x 3,088 merge_RSEM_output_to_matrix.pl
- - rwxr-xr-x 1,457 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 1,738 nameSorted_SAM_to_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 1,794 pairwise_kmer_content_comparer.pl
- - rwxr-xr-x 399 plot_ExN50_statistic.Rscript
- - rwxr-xr-x 814 plot_expressed_gene_dist.pl
- - rwxr-xr-x 867 print.pl
- - rwxr-xr-x 640 print_kmers.pl
- - rwxr-xr-x 2,420 process_GMAP_alignments_gff3_chimeras_ok.pl
- - rwxr-xr-x 1,986 prop_pair_sam_refiner.pl
- - rwxr-xr-x 105 remove_cntrl_chars.pl
- - rwxr-xr-x 306 row_to_column.pl
- - rwxr-xr-x 3,445 run_GSNAP.pl
- - rwxr-xr-x 4,454 run_HISAT.pl
- - rwxr-xr-x 1,207 run_HiCpipe_bowtie.pl
- - rwxr-xr-x 4,906 run_STAR.pl
- - rwxr-xr-x 1,858 run_TOPHAT.pl
- - rwxr-xr-x 939 run_bowtie2.pl
- - rwxr-xr-x 3,257 run_bwa.pl
- - rwxr-xr-x 1,152 run_bwasw_trinity.pl
- - rwxr-xr-x 1,406 run_jellyfish.pl
- - rwxr-xr-x 1,726 run_read_simulator_per_fasta_entry.pl
- - rwxr-xr-x 2,187 run_read_simulator_per_gene.pl
- - rwxr-xr-x 2,190 run_trimmomatic_qual_trimming.pl
- - rwxr-xr-x 212 shuffle.pl
- - rwxr-xr-x 8,731 simulate_illuminaPE_from_transcripts.pl
- - rwxr-xr-x 23,716 simulate_reads_sam_and_fa.pl
- - rwxr-xr-x 780 sixFrameTranslation.pl
- - rwxr-xr-x 1,190 sort_fastq.pl
- - rwxr-xr-x 442 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 4,606 transcript_coverage_UTR_trimmer.pl
- - rwxr-xr-x 5,825 transcript_fasta_to_ORF_pics.pl
- - rwxr-xr-x 2,005 transcript_gff3_to_bed.pl
- - rwxr-xr-x 1,500 transdecoder_pep_to_false_fusion_finder.pl
- - rwxr-xr-x 2,269 trinity_component_distribution.pl