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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: DifferentialExpression

d .. (parent)
d d rwxr-xr-x 4,096 R
d d rwxr-xr-x 4,096 TissueEnrichment
d d rwxr-xr-x 4,096 cluster_sample_data
d d rwxr-xr-x 4,096 pairwise_summaries
- - rwxr-xr-x 1,044 DE_graph_to_dot.pl
- - rwxr-xr-x 3,865 DTE_to_DTU.pl
- - rwxr-xr-x 2,993 GOplot.Rscript
- - rwxr-xr-x 3,203 Glimma.Trinity.Rscript
- - rwxr-xr-x 89,377 PtR
- - rwxr-xr-x 861 ROKU.pl
- - rwxr-xr-x 1,717 add_annot_to_trans_id.pl
- - rw-r--r-- 2,729 add_annotations_to_GO_and_lengths_file.R
- - rwxr-xr-x 1,074 add_blastx_hit_to_trinity_id.pl
- - rwxr-xr-x 19,476 analyze_diff_expr.pl
- - rwxr-xr-x 1,022 assign_tissue_specific.pl
- - rwxr-xr-x 5,925 compare_gene_trans_DE_ranks.pl
- - rwxr-xr-x 3,839 cut_tree_into_clusters.pl
- - rwxr-xr-x 6,867 define_clusters_by_cutting_tree.pl
- - rwxr-xr-x 3,934 diff_expr_analysis_to_heatmap_html.pl
- - rwxr-xr-x 5,995 diff_express.cgi
- - rwxr-xr-x 3,289 downsample_count_matrix.pl
- - rwxr-xr-x 3,887 extract_GO_enriched_genes.pl
- - rwxr-xr-x 1,043 filter_diff_expr.pl
- - rwxr-xr-x 518 filter_matrix_min_sum_rowcounts.pl
- - rwxr-xr-x 1,861 get_tissue_enriched_DE_one_vs_all.pl
- - rwxr-xr-x 505 get_transcript_lengths.pl
- - rwxr-xr-x 6,464 identify_diff_isoform_splicing.pl
- - rwxr-xr-x 957 log2_transform_matrix.pl
- - rwxr-xr-x 1,068 log2_transform_median_center_fpkm_matrix.pl
- - rwxr-xr-x 3,000 matrix_to_gene_plots.pl
- - rwxr-xr-x 2,204 merge_matrices.pl
- - rwxr-xr-x 494 merge_subclusters.pl
- - rwxr-xr-x 932 plot_all_DE_MAplots.Rscript
- - rwxr-xr-x 934 plot_all_DE_volcanos.Rscript
- - rwxr-xr-x 3,138 plot_expression_patterns.pl
- - rwxr-xr-x 239 plot_log2FC_hist.Rscript
- - rwxr-xr-x 6,984 prep_n_run_GOplot.pl
- - rwxr-xr-x 8,659 prune_isoforms_fasta.pl
- - rwxr-xr-x 1,918 prune_isoforms_gtf.pl
- - rwxr-xr-x 1,197 rank_roku_by_expr.pl
- - rwxr-xr-x 3,350 remove_batch_effects_from_count_matrix.pl
- - rwxr-xr-x 1,346 rename_matrix_column_labels.pl
- - rwxr-xr-x 1,330 rename_matrix_feature_identifiers.pl
- - rwxr-xr-x 4,629 replicates_to_sample_averages_matrix.pl
- - rwxr-xr-x 30,259 run_DE_analysis.pl
- - rwxr-xr-x 9,784 run_GOseq.pl
- - rwxr-xr-x 6,943 run_TMM_normalization_write_FPKM_matrix.pl
- - rwxr-xr-x 862 stratify_diff_expression.pl
- - rwxr-xr-x 537 subcluster_to_canvasXpress_html.make_index_html.pl
- - rwxr-xr-x 3,617 subcluster_to_canvasXpress_html.pl
- - rwxr-xr-x 1,430 summarize_diff_expr_across_min_threshold_ranges.pl
- - rwxr-xr-x 1,655 validate_UP_subset.Rscript