mirror of
https://github.com/BioArchLinux/Packages.git
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trinityrnaseq: rm patch
This commit is contained in:
parent
373c6068b4
commit
82f5af3d50
10 changed files with 4184 additions and 18 deletions
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@ -11,15 +11,13 @@ url="https://github.com/Trinotate/Trinotate/wiki"
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license=('BSD-3-Clause')
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license=('BSD-3-Clause')
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arch=('x86_64')
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arch=('x86_64')
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makedepends=('git' 'cmake' 'make' 'python' 'rsync')
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makedepends=('git' 'cmake' 'make' 'python' 'rsync')
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source=("git+https://github.com/trinityrnaseq/trinityrnaseq.git#tag=$_pkgname-v$pkgver"
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source=("git+https://github.com/trinityrnaseq/trinityrnaseq.git#tag=$_pkgname-v$pkgver")
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"string.patch")
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sha256sums=('3764a52e34eacdf4affc1ab719901e90c68e326b9be7b70a8bacdb8843e0aedf')
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sha256sums=('3764a52e34eacdf4affc1ab719901e90c68e326b9be7b70a8bacdb8843e0aedf'
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'9304eae411d76a6ce1846ed06e7311b35175638a74ec6277909ef9d4ba71769b')
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prepare(){
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prepare(){
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cd $srcdir/$pkgname
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cd $srcdir/$pkgname
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git submodule update --init --recursive
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git submodule update --init --recursive
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patch -p1 < $srcdir/string.patch
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# patch -p1 < $srcdir/string.patch
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}
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}
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build() {
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build() {
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@ -29,7 +27,8 @@ build() {
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}
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}
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package_trinityrnaseq() {
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package_trinityrnaseq() {
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depends=('perl' 'bash' 'glibc' 'java-runtime' 'python' 'zlib')
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depends=('perl' 'bash' 'glibc' 'java-runtime' 'python' 'zlib'
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'parafly' 'samtools' 'jellyfish' 'bowtie2' 'salmon')
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# 'xz' 'bzip2' 'curl'
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# 'xz' 'bzip2' 'curl'
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set -x
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set -x
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cd $srcdir/trinityrnaseq
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cd $srcdir/trinityrnaseq
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124
BioArchLinux/trinityrnaseq/analist
Normal file
124
BioArchLinux/trinityrnaseq/analist
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@ -0,0 +1,124 @@
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Analysis/DifferentialExpression/DE_graph_to_dot.pl
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Analysis/DifferentialExpression/DTE_to_DTU.pl
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Analysis/DifferentialExpression/GOplot.Rscript
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Analysis/DifferentialExpression/Glimma.Trinity.Rscript
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Analysis/DifferentialExpression/PtR
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Analysis/DifferentialExpression/ROKU.pl
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Analysis/DifferentialExpression/add_annot_to_trans_id.pl
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Analysis/DifferentialExpression/add_annotations_to_GO_and_lengths_file.R
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Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl
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Analysis/DifferentialExpression/analyze_diff_expr.pl
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Analysis/DifferentialExpression/assign_tissue_specific.pl
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Analysis/DifferentialExpression/compare_gene_trans_DE_ranks.pl
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Analysis/DifferentialExpression/cut_tree_into_clusters.pl
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Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
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Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
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Analysis/DifferentialExpression/diff_express.cgi
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Analysis/DifferentialExpression/downsample_count_matrix.pl
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Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
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Analysis/DifferentialExpression/filter_diff_expr.pl
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Analysis/DifferentialExpression/filter_matrix_min_sum_rowcounts.pl
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Analysis/DifferentialExpression/get_tissue_enriched_DE_one_vs_all.pl
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Analysis/DifferentialExpression/get_transcript_lengths.pl
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Analysis/DifferentialExpression/identify_diff_isoform_splicing.pl
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Analysis/DifferentialExpression/log2_transform_matrix.pl
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Analysis/DifferentialExpression/log2_transform_median_center_fpkm_matrix.pl
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Analysis/DifferentialExpression/matrix_to_gene_plots.pl
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Analysis/DifferentialExpression/merge_matrices.pl
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Analysis/DifferentialExpression/merge_subclusters.pl
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Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript
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Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript
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Analysis/DifferentialExpression/plot_expression_patterns.pl
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Analysis/DifferentialExpression/plot_log2FC_hist.Rscript
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Analysis/DifferentialExpression/prep_n_run_GOplot.pl
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Analysis/DifferentialExpression/prune_isoforms_fasta.pl
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Analysis/DifferentialExpression/prune_isoforms_gtf.pl
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Analysis/DifferentialExpression/rank_roku_by_expr.pl
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Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
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Analysis/DifferentialExpression/rename_matrix_column_labels.pl
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Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl
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Analysis/DifferentialExpression/replicates_to_sample_averages_matrix.pl
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Analysis/DifferentialExpression/run_DE_analysis.pl
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Analysis/DifferentialExpression/run_GOseq.pl
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Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
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Analysis/DifferentialExpression/stratify_diff_expression.pl
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Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.make_index_html.pl
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Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
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Analysis/DifferentialExpression/summarize_diff_expr_across_min_threshold_ranges.pl
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Analysis/DifferentialExpression/validate_UP_subset.Rscript
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Analysis/DifferentialExpression/R/edgeR.TMM.minimal.R
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Analysis/DifferentialExpression/R/edgeR_funcs.R
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Analysis/DifferentialExpression/R/get_cluster_info.R
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Analysis/DifferentialExpression/R/heatmap.3.R
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Analysis/DifferentialExpression/R/jaccard_distance.R
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Analysis/DifferentialExpression/R/manually_define_clusters.R
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Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R
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Analysis/DifferentialExpression/R/pairs3.R
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Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R
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Analysis/DifferentialExpression/R/test.heatmap.3.R
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Analysis/DifferentialExpression/R/vioplot2.R
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Analysis/DifferentialExpression/R/tests/test_heatmap_w_pca.R
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Analysis/DifferentialExpression/TissueEnrichment/DE_graph_to_dot.pl
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Analysis/DifferentialExpression/TissueEnrichment/DE_results_to_pairwise_summary.pl
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Analysis/DifferentialExpression/TissueEnrichment/README.md
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Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl
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Analysis/DifferentialExpression/TissueEnrichment/pairwise_DE_summary_to_DE_classification.pl
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Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
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Analysis/DifferentialExpression/cluster_sample_data/cleanme.pl
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Analysis/DifferentialExpression/cluster_sample_data/orig.samples.txt
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Analysis/DifferentialExpression/cluster_sample_data/runMe.sh
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Analysis/DifferentialExpression/cluster_sample_data/samples.txt
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Analysis/DifferentialExpression/cluster_sample_data/Islam_scde_data/es.mef.fpkm.matrix
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Analysis/DifferentialExpression/pairwise_summaries/DE_pair_counts_to_matrix.pl
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Analysis/DifferentialExpression/pairwise_summaries/EBSeq_to_pairwise_summary.pl
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Analysis/DifferentialExpression/pairwise_summaries/add_counts_to_classes.pl
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Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl
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Analysis/DifferentialExpression/pairwise_summaries/edgeR_to_pairwise_summary.pl
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Analysis/DifferentialExpression/pairwise_summaries/examine_rank_correlation.pl
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Analysis/DifferentialExpression/pairwise_summaries/extract_venn_agree_from_summaries.pl
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Analysis/DifferentialExpression/pairwise_summaries/mmdiff_to_pairwise_summary.pl
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Analysis/DifferentialExpression/pairwise_summaries/notes
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Analysis/DifferentialExpression/pairwise_summaries/pairwise_DE_summary_to_DE_classification.pl
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Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pair_stats.pl
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Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pl
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Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
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Analysis/FL_reconstruction_analysis/compute_oracle.pl
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Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl
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Analysis/FL_reconstruction_analysis/fusion_comparisons_via_maps_files.pl
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Analysis/FL_reconstruction_analysis/get_genes_from_maps_file.pl
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Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
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Analysis/FL_reconstruction_analysis/oracle_counter.pl
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Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
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Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl
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Analysis/FL_reconstruction_analysis/R/boot.tree.R
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Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
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Analysis/FL_reconstruction_analysis/util/blat_map_filter_with_isoforms.pl
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Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
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Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl
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Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
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Analysis/SuperTranscripts/README.md
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Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
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Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
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Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
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Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
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Analysis/SuperTranscripts/AllelicVariants/util/clean_bam.pl
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Analysis/SuperTranscripts/DTU/README.md
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Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
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Analysis/SuperTranscripts/DTU/util/reformat_featureCounts.pl
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Analysis/SuperTranscripts/_misc/aln_before_after.pl
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Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
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Analysis/SuperTranscripts/pylib/Compact_graph_pruner.py
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Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
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Analysis/SuperTranscripts/pylib/DP_matrix.py
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Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
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Analysis/SuperTranscripts/pylib/GraphCycleException.py
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Analysis/SuperTranscripts/pylib/Node_alignment.py
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Analysis/SuperTranscripts/pylib/Node_path.py
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Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
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Analysis/SuperTranscripts/pylib/TGLOBALS.py
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Analysis/SuperTranscripts/pylib/TGraph.py
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Analysis/SuperTranscripts/pylib/TNode.py
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Analysis/SuperTranscripts/pylib/Topological_sort.py
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Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
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Analysis/SuperTranscripts/pylib/Trinity_util.py
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Analysis/SuperTranscripts/pylib/__init__.py
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123
BioArchLinux/trinityrnaseq/analist.arch
Normal file
123
BioArchLinux/trinityrnaseq/analist.arch
Normal file
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@ -0,0 +1,123 @@
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Analysis/Compact_graph_partial.py
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Analysis/Compact_graph_pruner.py
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Analysis/Compact_graph_whole.py
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Analysis/DE_graph_to_dot.pl
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Analysis/DE_pair_counts_to_matrix.pl
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Analysis/DE_results_to_pairwise_summary.pl
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Analysis/DP_matrix.py
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Analysis/DTE_to_DTU.pl
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Analysis/EBSeq_to_pairwise_summary.pl
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Analysis/FL_trans_analysis_pipeline.pl
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Analysis/GOplot.Rscript
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Analysis/Gene_splice_modeler.py
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Analysis/Glimma.Trinity.Rscript
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Analysis/GraphCycleException.py
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Analysis/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
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Analysis/Node_alignment.py
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Analysis/Node_path.py
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Analysis/PtR
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Analysis/README.md
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Analysis/ROKU.pl
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Analysis/Splice_model_refiner.py
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Analysis/TGLOBALS.py
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Analysis/TGraph.py
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Analysis/TNode.py
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Analysis/Topological_sort.py
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Analysis/Trinity_fasta_parser.py
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Analysis/Trinity_gene_splice_modeler.py
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Analysis/Trinity_util.py
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Analysis/VCF_to_annotated_SNP_report.pl
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Analysis/__init__.py
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Analysis/add_annot_to_trans_id.pl
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Analysis/add_annotations_to_GO_and_lengths_file.R
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Analysis/add_blastx_hit_to_trinity_id.pl
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Analysis/add_counts_to_classes.pl
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Analysis/aln_before_after.pl
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Analysis/analyze_diff_expr.pl
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Analysis/assign_tissue_specific.pl
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Analysis/blat_full_length_mappings.pl
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Analysis/blat_map_filter_with_isoforms.pl
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Analysis/blat_psl_to_align_summary_stats.pl
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Analysis/blat_query_top_hit_extractor.pl
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Analysis/blat_top_tier_genes.pl
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Analysis/boot.tree.R
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Analysis/class_to_separate_fpkm_matrices.pl
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Analysis/clean_bam.pl
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Analysis/cleanme.pl
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Analysis/compare_gene_trans_DE_ranks.pl
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Analysis/compute_oracle.pl
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Analysis/count_by_expression_quintile.pl
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Analysis/cut_tree_into_clusters.pl
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Analysis/define_clusters_by_cutting_tree.pl
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Analysis/dexseq_wrapper.pl
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Analysis/diff_expr_analysis_to_heatmap_html.pl
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Analysis/diff_express.cgi
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Analysis/downsample_count_matrix.pl
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Analysis/edgeR.TMM.minimal.R
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Analysis/edgeR_funcs.R
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Analysis/edgeR_to_pairwise_summary.pl
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Analysis/es.mef.fpkm.matrix
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Analysis/examine_rank_correlation.pl
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Analysis/extract_GO_enriched_genes.pl
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Analysis/extract_supertranscript_from_reference.py
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Analysis/extract_venn_agree_from_summaries.pl
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Analysis/filter_diff_expr.pl
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Analysis/filter_matrix_min_sum_rowcounts.pl
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Analysis/fusion_comparisons_via_maps_files.pl
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Analysis/get_cluster_info.R
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Analysis/get_genes_from_maps_file.pl
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Analysis/get_tissue_enriched_DE_one_vs_all.pl
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Analysis/get_transcript_lengths.pl
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Analysis/group_isoforms_by_tissue_enrichment.pl
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Analysis/heatmap.3.R
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Analysis/identify_diff_isoform_splicing.pl
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Analysis/jaccard_distance.R
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Analysis/log2_transform_matrix.pl
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Analysis/log2_transform_median_center_fpkm_matrix.pl
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Analysis/manually_define_clusters.R
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Analysis/maps_file_to_paralog_representation.pl
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Analysis/matrix_to_gene_plots.pl
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Analysis/merge_matrices.pl
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Analysis/merge_subclusters.pl
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Analysis/misc_rnaseq_funcs.R
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Analysis/mmdiff_to_pairwise_summary.pl
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Analysis/notes
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Analysis/oracle_counter.pl
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Analysis/orig.samples.txt
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Analysis/pairs3.R
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Analysis/pairwise_DE_summary_to_DE_classification.pl
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Analysis/plot_all_DE_MAplots.Rscript
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Analysis/plot_all_DE_volcanos.Rscript
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Analysis/plot_expression_patterns.pl
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Analysis/plot_log2FC_hist.Rscript
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Analysis/prep_n_run_GOplot.pl
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Analysis/prune_isoforms_fasta.pl
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Analysis/prune_isoforms_gtf.pl
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Analysis/rank_roku_by_expr.pl
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Analysis/reformat_featureCounts.pl
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Analysis/remove_batch_effects_from_count_matrix.pl
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Analysis/rename_matrix_column_labels.pl
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Analysis/rename_matrix_feature_identifiers.pl
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Analysis/replicates_to_sample_averages_matrix.pl
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Analysis/rnaseq_plot_funcs.R
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Analysis/runMe.sh
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Analysis/run_DE_analysis.pl
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Analysis/run_GOseq.pl
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Analysis/run_TMM_normalization_write_FPKM_matrix.pl
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Analysis/run_variant_calling.py
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Analysis/samples.txt
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Analysis/stratify_diff_expression.pl
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Analysis/subcluster_to_canvasXpress_html.make_index_html.pl
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Analysis/subcluster_to_canvasXpress_html.pl
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Analysis/summarize_diff_expr_across_min_threshold_ranges.pl
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Analysis/test.heatmap.3.R
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Analysis/test.html
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Analysis/test_heatmap_w_pca.R
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Analysis/test_session.html
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Analysis/tier_gene_trans_alignments.pl
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Analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl
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Analysis/trinity_to_genomeview_html.pl
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Analysis/validate_UP_subset.Rscript
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Analysis/venn_pairwise_summaries.pair_stats.pl
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Analysis/venn_pairwise_summaries.pl
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Analysis/vioplot2.R
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505
BioArchLinux/trinityrnaseq/archlist
Normal file
505
BioArchLinux/trinityrnaseq/archlist
Normal file
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@ -0,0 +1,505 @@
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Analysis/Compact_graph_partial.py
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Analysis/Compact_graph_pruner.py
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Analysis/Compact_graph_whole.py
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Analysis/DE_graph_to_dot.pl
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Analysis/DE_pair_counts_to_matrix.pl
|
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Analysis/DE_results_to_pairwise_summary.pl
|
||||||
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Analysis/DP_matrix.py
|
||||||
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Analysis/DTE_to_DTU.pl
|
||||||
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Analysis/EBSeq_to_pairwise_summary.pl
|
||||||
|
Analysis/FL_trans_analysis_pipeline.pl
|
||||||
|
Analysis/GOplot.Rscript
|
||||||
|
Analysis/Gene_splice_modeler.py
|
||||||
|
Analysis/Glimma.Trinity.Rscript
|
||||||
|
Analysis/GraphCycleException.py
|
||||||
|
Analysis/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
|
||||||
|
Analysis/Node_alignment.py
|
||||||
|
Analysis/Node_path.py
|
||||||
|
Analysis/PtR
|
||||||
|
Analysis/README.md
|
||||||
|
Analysis/ROKU.pl
|
||||||
|
Analysis/Splice_model_refiner.py
|
||||||
|
Analysis/TGLOBALS.py
|
||||||
|
Analysis/TGraph.py
|
||||||
|
Analysis/TNode.py
|
||||||
|
Analysis/Topological_sort.py
|
||||||
|
Analysis/Trinity_fasta_parser.py
|
||||||
|
Analysis/Trinity_gene_splice_modeler.py
|
||||||
|
Analysis/Trinity_util.py
|
||||||
|
Analysis/VCF_to_annotated_SNP_report.pl
|
||||||
|
Analysis/__init__.py
|
||||||
|
Analysis/add_annot_to_trans_id.pl
|
||||||
|
Analysis/add_annotations_to_GO_and_lengths_file.R
|
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|
Analysis/add_blastx_hit_to_trinity_id.pl
|
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Analysis/add_counts_to_classes.pl
|
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Analysis/aln_before_after.pl
|
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Analysis/analyze_diff_expr.pl
|
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Analysis/assign_tissue_specific.pl
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Analysis/blat_full_length_mappings.pl
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Analysis/blat_map_filter_with_isoforms.pl
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Analysis/blat_psl_to_align_summary_stats.pl
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Analysis/blat_query_top_hit_extractor.pl
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Analysis/blat_top_tier_genes.pl
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Analysis/boot.tree.R
|
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Analysis/class_to_separate_fpkm_matrices.pl
|
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Analysis/clean_bam.pl
|
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Analysis/cleanme.pl
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Analysis/compare_gene_trans_DE_ranks.pl
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Analysis/compute_oracle.pl
|
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Analysis/count_by_expression_quintile.pl
|
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Analysis/cut_tree_into_clusters.pl
|
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Analysis/define_clusters_by_cutting_tree.pl
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Analysis/dexseq_wrapper.pl
|
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Analysis/diff_expr_analysis_to_heatmap_html.pl
|
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Analysis/diff_express.cgi
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Analysis/downsample_count_matrix.pl
|
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Analysis/edgeR.TMM.minimal.R
|
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Analysis/edgeR_funcs.R
|
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Analysis/edgeR_to_pairwise_summary.pl
|
||||||
|
Analysis/es.mef.fpkm.matrix
|
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|
Analysis/examine_rank_correlation.pl
|
||||||
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Analysis/extract_GO_enriched_genes.pl
|
||||||
|
Analysis/extract_supertranscript_from_reference.py
|
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|
Analysis/extract_venn_agree_from_summaries.pl
|
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|
Analysis/filter_diff_expr.pl
|
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Analysis/filter_matrix_min_sum_rowcounts.pl
|
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|
Analysis/fusion_comparisons_via_maps_files.pl
|
||||||
|
Analysis/get_cluster_info.R
|
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|
Analysis/get_genes_from_maps_file.pl
|
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|
Analysis/get_tissue_enriched_DE_one_vs_all.pl
|
||||||
|
Analysis/get_transcript_lengths.pl
|
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|
Analysis/group_isoforms_by_tissue_enrichment.pl
|
||||||
|
Analysis/heatmap.3.R
|
||||||
|
Analysis/identify_diff_isoform_splicing.pl
|
||||||
|
Analysis/jaccard_distance.R
|
||||||
|
Analysis/log2_transform_matrix.pl
|
||||||
|
Analysis/log2_transform_median_center_fpkm_matrix.pl
|
||||||
|
Analysis/manually_define_clusters.R
|
||||||
|
Analysis/maps_file_to_paralog_representation.pl
|
||||||
|
Analysis/matrix_to_gene_plots.pl
|
||||||
|
Analysis/merge_matrices.pl
|
||||||
|
Analysis/merge_subclusters.pl
|
||||||
|
Analysis/misc_rnaseq_funcs.R
|
||||||
|
Analysis/mmdiff_to_pairwise_summary.pl
|
||||||
|
Analysis/notes
|
||||||
|
Analysis/oracle_counter.pl
|
||||||
|
Analysis/orig.samples.txt
|
||||||
|
Analysis/pairs3.R
|
||||||
|
Analysis/pairwise_DE_summary_to_DE_classification.pl
|
||||||
|
Analysis/plot_all_DE_MAplots.Rscript
|
||||||
|
Analysis/plot_all_DE_volcanos.Rscript
|
||||||
|
Analysis/plot_expression_patterns.pl
|
||||||
|
Analysis/plot_log2FC_hist.Rscript
|
||||||
|
Analysis/prep_n_run_GOplot.pl
|
||||||
|
Analysis/prune_isoforms_fasta.pl
|
||||||
|
Analysis/prune_isoforms_gtf.pl
|
||||||
|
Analysis/rank_roku_by_expr.pl
|
||||||
|
Analysis/reformat_featureCounts.pl
|
||||||
|
Analysis/remove_batch_effects_from_count_matrix.pl
|
||||||
|
Analysis/rename_matrix_column_labels.pl
|
||||||
|
Analysis/rename_matrix_feature_identifiers.pl
|
||||||
|
Analysis/replicates_to_sample_averages_matrix.pl
|
||||||
|
Analysis/rnaseq_plot_funcs.R
|
||||||
|
Analysis/runMe.sh
|
||||||
|
Analysis/run_DE_analysis.pl
|
||||||
|
Analysis/run_GOseq.pl
|
||||||
|
Analysis/run_TMM_normalization_write_FPKM_matrix.pl
|
||||||
|
Analysis/run_variant_calling.py
|
||||||
|
Analysis/samples.txt
|
||||||
|
Analysis/stratify_diff_expression.pl
|
||||||
|
Analysis/subcluster_to_canvasXpress_html.make_index_html.pl
|
||||||
|
Analysis/subcluster_to_canvasXpress_html.pl
|
||||||
|
Analysis/summarize_diff_expr_across_min_threshold_ranges.pl
|
||||||
|
Analysis/test.heatmap.3.R
|
||||||
|
Analysis/test.html
|
||||||
|
Analysis/test_heatmap_w_pca.R
|
||||||
|
Analysis/test_session.html
|
||||||
|
Analysis/tier_gene_trans_alignments.pl
|
||||||
|
Analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl
|
||||||
|
Analysis/trinity_to_genomeview_html.pl
|
||||||
|
Analysis/validate_UP_subset.Rscript
|
||||||
|
Analysis/venn_pairwise_summaries.pair_stats.pl
|
||||||
|
Analysis/venn_pairwise_summaries.pl
|
||||||
|
Analysis/vioplot2.R
|
||||||
|
PerlLib/
|
||||||
|
PerlLib/AlignGraph.pm
|
||||||
|
PerlLib/AlignNode.pm
|
||||||
|
PerlLib/Alignment_segment.pm
|
||||||
|
PerlLib/Alternative_splice_comparer.pm
|
||||||
|
PerlLib/Ascii_genome_illustrator.pm
|
||||||
|
PerlLib/BED_utils.pm
|
||||||
|
PerlLib/BHStats.pm
|
||||||
|
PerlLib/CDNA_alignment.pm
|
||||||
|
PerlLib/CDNA_stitcher.pm
|
||||||
|
PerlLib/CIGAR.pm
|
||||||
|
PerlLib/CMD_processor.pm
|
||||||
|
PerlLib/COMMON.pm
|
||||||
|
PerlLib/ColorGradient.pm
|
||||||
|
PerlLib/DelimParser.pm
|
||||||
|
PerlLib/EM.pm
|
||||||
|
PerlLib/Exons_to_geneobj.pm
|
||||||
|
PerlLib/Fasta_reader.pm
|
||||||
|
PerlLib/Fasta_retriever.pm
|
||||||
|
PerlLib/Fastq_reader.pm
|
||||||
|
PerlLib/GFF3_alignment_utils.pm
|
||||||
|
PerlLib/GFF3_utils.pm
|
||||||
|
PerlLib/GFF_maker.pm
|
||||||
|
PerlLib/GTF.pm
|
||||||
|
PerlLib/GTF_utils.pm
|
||||||
|
PerlLib/Gene_obj.pm
|
||||||
|
PerlLib/Gene_obj_alignment_assembler.pm
|
||||||
|
PerlLib/Gene_obj_indexer.pm
|
||||||
|
PerlLib/GenericGraph.pm
|
||||||
|
PerlLib/GenericNode.pm
|
||||||
|
PerlLib/Genome_based_cDNA_assembler.pm
|
||||||
|
PerlLib/Genome_based_cDNA_graph_assembler.pm
|
||||||
|
PerlLib/Heatmap.pm
|
||||||
|
PerlLib/KmerGraph.pm
|
||||||
|
PerlLib/KmerNode.pm
|
||||||
|
PerlLib/Ktree.pm
|
||||||
|
PerlLib/Longest_orf.pm
|
||||||
|
PerlLib/Nuc_translator.pm
|
||||||
|
PerlLib/Overlap_assembler.pm
|
||||||
|
PerlLib/Overlap_info.pm
|
||||||
|
PerlLib/Overlap_piler.pm
|
||||||
|
PerlLib/PASA_alignment_assembler.pm
|
||||||
|
PerlLib/PSL_parser.pm
|
||||||
|
PerlLib/Pipeliner.pm
|
||||||
|
PerlLib/Process_cmd.pm
|
||||||
|
PerlLib/ReadCoverageGraph.pm
|
||||||
|
PerlLib/ReadCoverageNode.pm
|
||||||
|
PerlLib/ReadManager.pm
|
||||||
|
PerlLib/ReadTracker.pm
|
||||||
|
PerlLib/SAM_entry.pm
|
||||||
|
PerlLib/SAM_reader.pm
|
||||||
|
PerlLib/SAM_to_AlignGraph.pm
|
||||||
|
PerlLib/SingleLinkageClusterer.pm
|
||||||
|
PerlLib/Splice_graph_assembler.pm
|
||||||
|
PerlLib/StringGraph.pm
|
||||||
|
PerlLib/StringNode.pm
|
||||||
|
PerlLib/Thread_helper.pm
|
||||||
|
PerlLib/TiedHash.pm
|
||||||
|
PerlLib/Uniform_Read_Generator.pm
|
||||||
|
PerlLib/VCF_parser.pm
|
||||||
|
PerlLib/WigParser.pm
|
||||||
|
PerlLib/overlapping_nucs.ph
|
||||||
|
PerlLib/test_Fasta_retriever.pl
|
||||||
|
PerlLib/test_htc_gridrunner_LSF.pl
|
||||||
|
PerlLib/test_htc_gridrunner_SGE.pl
|
||||||
|
PyLib/
|
||||||
|
PyLib/Pipeliner.py
|
||||||
|
Trinity
|
||||||
|
trinity-plugins/
|
||||||
|
trinity-plugins/COLLECTL/
|
||||||
|
trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
|
||||||
|
trinity-plugins/COLLECTL/util/
|
||||||
|
trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py
|
||||||
|
trinity-plugins/COLLECTL/util/plot_time_vs_resource.Rscript
|
||||||
|
trinity-plugins/DEXseq_util/
|
||||||
|
trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
|
||||||
|
trinity-plugins/bamsifter/
|
||||||
|
trinity-plugins/bamsifter/bamsifter
|
||||||
|
util/
|
||||||
|
util/ButterflyFastaToGraphDot.pl
|
||||||
|
util/ExitTester.jar
|
||||||
|
util/GG_partitioned_trinity_aggregator.pl
|
||||||
|
util/HiCpipe_nameSortedSam_to_raw.pl
|
||||||
|
util/Monarch
|
||||||
|
util/N50.pl
|
||||||
|
util/N50stats.pl
|
||||||
|
util/README
|
||||||
|
util/SAM_coordSorted_fragment_Read_coverage_writer.pl
|
||||||
|
util/SAM_coordSorted_fragment_coverage_writer2.pl
|
||||||
|
util/SAM_coordsorted_max_reads_per_position.pl
|
||||||
|
util/SAM_extract_properly_mapped_pairs.pl
|
||||||
|
util/SAM_extract_uniquely_mapped_reads.pl
|
||||||
|
util/SAM_filter_out_unmapped_reads.pl
|
||||||
|
util/SAM_intron_extractor.pl
|
||||||
|
util/SAM_nameSorted_to_uniq_count_stats.pl
|
||||||
|
util/SAM_ordered_pair_jaccard.pl
|
||||||
|
util/SAM_pair_to_bed.pl
|
||||||
|
util/SAM_set_transcribed_orient_info.pl
|
||||||
|
util/SAM_show_alignment.pl
|
||||||
|
util/SAM_show_alignment.summarize_stats.pl
|
||||||
|
util/SAM_sortAny_to_count_stats.pl
|
||||||
|
util/SAM_strand_separator.pl
|
||||||
|
util/SAM_toString.pl
|
||||||
|
util/SAM_to_bed.pl
|
||||||
|
util/SAM_to_fasta.pl
|
||||||
|
util/SAM_to_frag_coords.pl
|
||||||
|
util/SAM_to_gff3.minimap2.pl
|
||||||
|
util/SRA_to_fastq.notes
|
||||||
|
util/SRA_to_fastq.pl
|
||||||
|
util/STAR_align_log_parser.py
|
||||||
|
util/SegmentGraph.pm
|
||||||
|
util/TPM_weighted_gene_length.py
|
||||||
|
util/TRINITY.CONFIG.template
|
||||||
|
util/TophatCufflinksWrapper.pl
|
||||||
|
util/TrinityStats.pl
|
||||||
|
util/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
|
||||||
|
util/Trinity_node_seq_extractor.pl
|
||||||
|
util/abundance_estimates_to_matrix.pl
|
||||||
|
util/acc_list_to_fasta_entries.pl
|
||||||
|
util/add_LR_reads_to_iworm_bundle.pl
|
||||||
|
util/alexie_analyze_blast.pl
|
||||||
|
util/align_and_estimate_abundance.pl
|
||||||
|
util/align_reads_launch_igv.pl
|
||||||
|
util/allele_simulator.pl
|
||||||
|
util/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
|
||||||
|
util/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
|
||||||
|
util/analyze_blastPlus_topHit_coverage.extract_OS.pl
|
||||||
|
util/analyze_blastPlus_topHit_coverage.org_matrix.pl
|
||||||
|
util/analyze_blastPlus_topHit_coverage.pl
|
||||||
|
util/annotate_chrysalis_welds_with_iworm_names.pl
|
||||||
|
util/assess_intron_path_sensitivity.pl
|
||||||
|
util/assess_intron_path_sensitivity.summarizer.pl
|
||||||
|
util/audit_summary_stats.pl
|
||||||
|
util/audit_summary_stats.reexamine.pl
|
||||||
|
util/average.pl
|
||||||
|
util/bam_to_cuff.pl
|
||||||
|
util/batch_cmds.pl
|
||||||
|
util/blast_outfmt6_group_segments.pl
|
||||||
|
util/blast_outfmt6_group_segments.to_Markov_Clustering.pl
|
||||||
|
util/blast_outfmt6_group_segments.tophit_coverage.pl
|
||||||
|
util/blastn_wrapper.pl
|
||||||
|
util/blat_sam_add_reads2.pl
|
||||||
|
util/blat_to_sam.pl
|
||||||
|
util/blat_top_hit_extractor.pl
|
||||||
|
util/bowtie2_wrapper.pl
|
||||||
|
util/capture_orig_n_unmapped_reads.pl
|
||||||
|
util/cat_require_newlines.pl
|
||||||
|
util/cdhit_examine_isoforms.pl
|
||||||
|
util/cdna_fasta_file_to_transcript_gtf.pl
|
||||||
|
util/check_chrysalis_graph_reciprocal_edges.pl
|
||||||
|
util/check_fastQ_pair_ordering.pl
|
||||||
|
util/chrys_graph_to_dot.pl
|
||||||
|
util/collate_fqs.pl
|
||||||
|
util/combined_nameSorted_to_dup_pairs_removed.pl
|
||||||
|
util/compare_FL_stats.pl
|
||||||
|
util/compare_bflies.pl
|
||||||
|
util/component_to_graph_dot.pl
|
||||||
|
util/contig_ExN50_statistic.pl
|
||||||
|
util/convert_fasta_identifiers_for_FL_analysis.pl
|
||||||
|
util/count_N50_given_MIN_FPKM_threshold.pl
|
||||||
|
util/count_features_given_MIN_FPKM_threshold.pl
|
||||||
|
util/count_iso_per_gene_dist.pl
|
||||||
|
util/count_matrix_features_given_MIN_TPM_threshold.pl
|
||||||
|
util/count_number_fasta_seqs.pl
|
||||||
|
util/count_trans_per_component.pl
|
||||||
|
util/cuff_gtf_to_bed.pl
|
||||||
|
util/decode_SAM_flag_value.pl
|
||||||
|
util/define_SAM_coverage_partitions2.pl
|
||||||
|
util/define_coverage_partitions.pl
|
||||||
|
util/describe_SAM_read_flag_info.pl
|
||||||
|
util/determine_RF_strand_specificity.pl
|
||||||
|
util/diff_splice_paths.pl
|
||||||
|
util/eXpress_trans_to_gene_results.pl
|
||||||
|
util/ensure_coord_sorted_sam.pl
|
||||||
|
util/ensure_paired_end_bam_file.pl
|
||||||
|
util/examine_iworm_FL_across_threads.pl
|
||||||
|
util/examine_strand_specificity.pl
|
||||||
|
util/examine_weldmer_halves.pl
|
||||||
|
util/expression_analysis_lib.R
|
||||||
|
util/extract_bam_reads_per_target_gene.pl
|
||||||
|
util/extract_bam_reads_per_target_transcript.pl
|
||||||
|
util/extract_fastQ_pairings.pl
|
||||||
|
util/extract_reads_per_partition.pl
|
||||||
|
util/fan_out_fasta_seqs_to_indiv_files.pl
|
||||||
|
util/fastQ_append_acc.pl
|
||||||
|
util/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
|
||||||
|
util/fastQ_rand_subset.pl
|
||||||
|
util/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
|
||||||
|
util/fastQ_to_fastA.pl
|
||||||
|
util/fastQ_to_tab.pl
|
||||||
|
util/fastQ_top_N_records.pl
|
||||||
|
util/fasta_file_reformatter.pl
|
||||||
|
util/fasta_filter_by_min_length.pl
|
||||||
|
util/fasta_find_duplicates.pl
|
||||||
|
util/fasta_remove_duplicates.pl
|
||||||
|
util/fasta_seq_length.pl
|
||||||
|
util/fasta_to_cmd_generator.pl
|
||||||
|
util/fasta_to_tab.pl
|
||||||
|
util/fasta_write_sense_n_anti.pl
|
||||||
|
util/fastq_cleaner.pl
|
||||||
|
util/fastq_interleave_pairs.pl
|
||||||
|
util/fastq_merge_sorted_tab_lists.pl
|
||||||
|
util/fastq_stats.pl
|
||||||
|
util/fastq_unweave_pairs.pl
|
||||||
|
util/filter_iworm_by_min_length_or_cov.pl
|
||||||
|
util/filter_low_expr_transcripts.pl
|
||||||
|
util/filter_out_accs_from_fasta.pl
|
||||||
|
util/filter_similar_seqs_expr_and_strand_aware.pl
|
||||||
|
util/filter_transcripts_require_min_cov.pl
|
||||||
|
util/find_pruned_edges_shouldve_kept.pl
|
||||||
|
util/flattened_gff_n_genome_to_Trinity_emulator.pl
|
||||||
|
util/frag_boundary_to_wig.pl
|
||||||
|
util/frag_to_bed.pl
|
||||||
|
util/fragment_coverage_writer.pl
|
||||||
|
util/gene_gff3_to_bed_cmds.pl
|
||||||
|
util/gene_gff3_to_introns.pl
|
||||||
|
util/gene_to_shared_transcript_content.pl
|
||||||
|
util/generate_gene_alt_splicing_graphs.pl
|
||||||
|
util/generate_trans_graphs.pl
|
||||||
|
util/genome_gff3_to_gene_gff3_partitions.pl
|
||||||
|
util/genwig.sh
|
||||||
|
util/genwig2.py
|
||||||
|
util/get_GC_content_dist.pl
|
||||||
|
util/get_Poisson_conf_intervals.R
|
||||||
|
util/get_Trinity_gene_to_trans_map.pl
|
||||||
|
util/get_longest_isoform_seq_per_trinity_gene.pl
|
||||||
|
util/get_path_nodes_from_fasta.pl
|
||||||
|
util/get_welds_from_chrysals_graphFromFasta_out.pl
|
||||||
|
util/gff3_file_to_cdna.pl
|
||||||
|
util/gff3_file_utr_coverage_trimmer.pl
|
||||||
|
util/gff3_to_genome_feature_base_encoding.parse_SAM.pl
|
||||||
|
util/gff3_to_genome_feature_base_encoding.pl
|
||||||
|
util/gmap_gff3_chimera_jaccard_analyzer.pl
|
||||||
|
util/gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
|
||||||
|
util/gmap_gff3_to_percent_length_stats.pl
|
||||||
|
util/gmap_native_to_format_converter.pl
|
||||||
|
util/gmap_to_ref.pl
|
||||||
|
util/graph_out_to_bfly_cmd.pl
|
||||||
|
util/gtf_to_bed_format.pl
|
||||||
|
util/gtf_to_introns.pl
|
||||||
|
util/harvest_transcripts.pl
|
||||||
|
util/hicpipe_raw_converter.pl
|
||||||
|
util/identify_distal_isoform_variations.pl
|
||||||
|
util/illustrate_ref_comparison.pl
|
||||||
|
util/inchworm_transcript_splitter.pl
|
||||||
|
util/info_files_to_eval_cmds.pl
|
||||||
|
util/insilico_read_normalization.pl
|
||||||
|
util/intron_barcharter.pl
|
||||||
|
util/iworm_LR_to_scaff_pairs.pl
|
||||||
|
util/iworm_welds_to_dot.pl
|
||||||
|
util/jaccard_fasta_clipper.pl
|
||||||
|
util/jaccard_sam_pair_refiner.pl
|
||||||
|
util/jaccard_wig_clipper.pl
|
||||||
|
util/join_any.pl
|
||||||
|
util/join_by_left_col.pl
|
||||||
|
util/join_expr_vals_single_table.pl
|
||||||
|
util/join_multi_wig_to_graph_plot.pl
|
||||||
|
util/join_partitions_within_range.pl
|
||||||
|
util/kallisto_trans_to_gene_results.pl
|
||||||
|
util/kmer_counter.pl
|
||||||
|
util/kmer_histo.NormMaxKCov50.txt
|
||||||
|
util/kmer_histo.all.txt
|
||||||
|
util/m8_blastclust.pl
|
||||||
|
util/map_gtf_transcripts_to_genome_annots.pl
|
||||||
|
util/merge_RSEM_output_to_matrix.pl
|
||||||
|
util/merge_blast_n_rsem_results.pl
|
||||||
|
util/merge_pair_and_LR_scaff_links.pl
|
||||||
|
util/merge_replicate_bams_via_samples_file.pl
|
||||||
|
util/merge_rsem_n_express_for_compare.pl
|
||||||
|
util/mpi_iworm_proc_contigs_to_fa.pl
|
||||||
|
util/nameSorted_SAM_to_FastQ.pl
|
||||||
|
util/nameSorted_SAM_to_paired_fastq.pl
|
||||||
|
util/nbkc_merge_left_right_stats.pl
|
||||||
|
util/nbkc_normalize.pl
|
||||||
|
util/notes
|
||||||
|
util/omp_iworm_thread_contigs_to_fa.pl
|
||||||
|
util/ordered_fragment_coords_to_jaccard.pl
|
||||||
|
util/organize_data_table_by_trinity_component.pl
|
||||||
|
util/outfmt6_add_percent_match_length.pl
|
||||||
|
util/pair_up_fastq_files_1_2.pl
|
||||||
|
util/pair_up_fastq_files_LeftRight.pl
|
||||||
|
util/pair_up_fastq_files_R1_R2.pl
|
||||||
|
util/pairwise_kmer_content_comparer.pl
|
||||||
|
util/partition_chrysalis_graphs_n_reads.pl
|
||||||
|
util/partition_target_transcripts.pl
|
||||||
|
util/partitioned_trinity_aggregator.pl
|
||||||
|
util/pbs_check.pl
|
||||||
|
util/plot_ExN50_statistic.Rscript
|
||||||
|
util/plot_expressed_gene_dist.pl
|
||||||
|
util/plot_me.R
|
||||||
|
util/plot_strand_specificity_dist_by_quantile.Rscript
|
||||||
|
util/plugin_install_tests.sh
|
||||||
|
util/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
|
||||||
|
util/print.pl
|
||||||
|
util/print_butterfly_assemblies.pl
|
||||||
|
util/print_kmers.pl
|
||||||
|
util/process_BLAT_alignments.pl
|
||||||
|
util/process_GMAP_alignments_gff3_chimeras_ok.pl
|
||||||
|
util/process_minimap2_alignments.pl
|
||||||
|
util/prop_pair_sam_refiner.pl
|
||||||
|
util/pslx_to_gff3.pl
|
||||||
|
util/randomly_mutate_seqs.pl
|
||||||
|
util/randomly_sample_PE_fastq.pl
|
||||||
|
util/remove_cntrl_chars.pl
|
||||||
|
util/rename_fasta_accessions_using_Trinotate_annot_mappings.pl
|
||||||
|
util/result.pdf
|
||||||
|
util/retrieve_sequences_from_fasta.pl
|
||||||
|
util/revcomp_fasta.pl
|
||||||
|
util/row_to_column.pl
|
||||||
|
util/run_BLAT_shortReads.pl
|
||||||
|
util/run_DETONATE.pl
|
||||||
|
util/run_GSNAP.pl
|
||||||
|
util/run_HISAT.pl
|
||||||
|
util/run_HISAT2_via_samples_file.pl
|
||||||
|
util/run_HiCpipe_bowtie.pl
|
||||||
|
util/run_STAR.pl
|
||||||
|
util/run_STAR_via_samples_file.pl
|
||||||
|
util/run_Stringtie_via_bam_file_list.pl
|
||||||
|
util/run_TMM_scale_matrix.pl
|
||||||
|
util/run_TOPHAT.pl
|
||||||
|
util/run_Trinity_eval.pl
|
||||||
|
util/run_Trinity_eval.sh
|
||||||
|
util/run_UpperQuartileNormalization_matrix.pl
|
||||||
|
util/run_bowtie2.pl
|
||||||
|
util/run_bwa.pl
|
||||||
|
util/run_bwasw_trinity.pl
|
||||||
|
util/run_jellyfish.pl
|
||||||
|
util/run_read_simulator_per_fasta_entry.pl
|
||||||
|
util/run_read_simulator_per_gene.pl
|
||||||
|
util/run_simulate_reads.wgsim.pl
|
||||||
|
util/run_trimmomatic_qual_trimming.pl
|
||||||
|
util/run_trinity_WITH_LR.pl
|
||||||
|
util/run_trinity_no_LR.pl
|
||||||
|
util/salmon_runner.pl
|
||||||
|
util/salmon_trans_to_gene_results.pl
|
||||||
|
util/sample_data_tests.py
|
||||||
|
util/scaffold_iworm_contigs.pl
|
||||||
|
util/segment_GFF_partitions.pl
|
||||||
|
util/seqinfo_refseq_to_dot.pl
|
||||||
|
util/shuffle.pl
|
||||||
|
util/sift_bam_max_cov.pl
|
||||||
|
util/sim_reads.pl
|
||||||
|
util/sim_single_bubble.pl
|
||||||
|
util/simulate_illuminaPE_from_transcripts.pl
|
||||||
|
util/simulate_illuminaPE_from_transcripts.wgsim.pl
|
||||||
|
util/simulate_reads_sam_and_fa.pl
|
||||||
|
util/sixFrameTranslation.pl
|
||||||
|
util/sort_fastq.pl
|
||||||
|
util/strip_fasta_header.pl
|
||||||
|
util/tab_to_fastQ.pl
|
||||||
|
util/tab_to_fasta.pl
|
||||||
|
util/tblastn_wrapper.pl
|
||||||
|
util/testUnlimitStacksize.pl
|
||||||
|
util/test_prep.py
|
||||||
|
util/tests.py
|
||||||
|
util/top_blat_sam_extractor.pl
|
||||||
|
util/trans_gff3_to_bed_cmds.pl
|
||||||
|
util/transcript_coverage_UTR_trimmer.pl
|
||||||
|
util/transcript_fasta_to_ORF_pics.pl
|
||||||
|
util/transcript_gff3_to_bed.pl
|
||||||
|
util/transdecoder_pep_to_false_fusion_finder.pl
|
||||||
|
util/trinity_component_distribution.pl
|
||||||
|
util/trinity_install_tests.sh
|
||||||
|
util/trinity_installer.py
|
||||||
|
util/trinity_kill.pl
|
||||||
|
util/trinity_kill.sh
|
||||||
|
util/trinity_pbs.cont
|
||||||
|
util/trinity_pbs.header
|
||||||
|
util/trinity_pbs.p1
|
||||||
|
util/trinity_pbs.p2
|
||||||
|
util/trinity_pbs.p3
|
||||||
|
util/trinity_pbs.p4a
|
||||||
|
util/trinity_pbs.p4b
|
||||||
|
util/trinity_pbs.p5b
|
||||||
|
util/trinity_pbs.sh
|
||||||
|
util/trinity_trans_matrix_to_rep_trans_gene_matrix.pl
|
||||||
|
util/try_estimate_TPM_filtering_threshold.Rscript
|
||||||
|
util/validate_fastqs.py
|
||||||
|
util/wig_clip_to_bed.pl
|
||||||
|
util/write_partitioned_trinity_cmds.pl
|
||||||
|
util/write_simulate_read_commands.pl
|
||||||
|
util/write_trin_cmds.pl
|
||||||
90
BioArchLinux/trinityrnaseq/butterfly.patch
Normal file
90
BioArchLinux/trinityrnaseq/butterfly.patch
Normal file
|
|
@ -0,0 +1,90 @@
|
||||||
|
Description: Updates the main Trinity program to use FHS paths
|
||||||
|
Author: Michael R. Crusoe <crusoe@debian.org>
|
||||||
|
Forwarded: not-needed
|
||||||
|
Last-Updated: 2015-02-22
|
||||||
|
|
||||||
|
--- trinityrnaseq.orig/Trinity
|
||||||
|
+++ trinityrnaseq/Trinity
|
||||||
|
@@ -381,7 +381,7 @@
|
||||||
|
# --bfly_algorithm <string> : assembly algorithm to use. Options: @BFLY_ALGORITHMS
|
||||||
|
#
|
||||||
|
# --bfly_opts <string> :additional parameters to pass through to butterfly
|
||||||
|
-# (see butterfly options: java -jar Butterfly.jar ).
|
||||||
|
+# (see butterfly options: java -jar /usr/share/java/Butterfly.jar ).
|
||||||
|
# (note: only for expert or experimental use. Commonly used parameters are exposed through this Trinity menu here).
|
||||||
|
#
|
||||||
|
#
|
||||||
|
@@ -1074,7 +1074,7 @@
|
||||||
|
}
|
||||||
|
|
||||||
|
unless ($BFLY_JAR) {
|
||||||
|
- $BFLY_JAR = "$BUTTERFLY_DIR/Butterfly.jar";
|
||||||
|
+ $BFLY_JAR = "/usr/share/java/Butterfly.jar";
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
--- trinityrnaseq.orig/Chrysalis/analysis/Chrysalis.cc
|
||||||
|
+++ trinityrnaseq/Chrysalis/analysis/Chrysalis.cc
|
||||||
|
@@ -258,7 +258,7 @@
|
||||||
|
commandArg<string> iwormStringCmmd("-iworm","inchworm file", "");
|
||||||
|
commandArg<string> oStringCmmd("-o","output directory");
|
||||||
|
commandArg<bool> pairsStringCmmd("-paired", "paired-end reads are used.", false);
|
||||||
|
- commandArg<string> butterflyCmmd("-butterfly","butterfly executable", "../Butterfly/Butterfly.jar");
|
||||||
|
+ commandArg<string> butterflyCmmd("-butterfly","butterfly executable", "/usr/share/java/Butterfly.jar");
|
||||||
|
commandArg<bool> skipCmmd("-skip","skip initial 2 steps", false);
|
||||||
|
commandArg<bool> strandCmmd("-strand","strand-specific data", false);
|
||||||
|
commandArg<bool> nobreakCmmd("-nobreak","skip breaking", false);
|
||||||
|
--- trinityrnaseq.orig/trinity-plugins/bamsifter/Makefile
|
||||||
|
+++ trinityrnaseq/trinity-plugins/bamsifter/Makefile
|
||||||
|
@@ -3,7 +3,7 @@
|
||||||
|
cwd = $(shell pwd)
|
||||||
|
|
||||||
|
sift_bam_max_cov: sift_bam_max_cov.cpp htslib/version.h
|
||||||
|
- g++ -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts
|
||||||
|
+ $(CXX) $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) -std=c++11 -o _sift_bam_max_cov sift_bam_max_cov.cpp -Wall -O2 -L./htslib/build/lib/ -I./htslib/build/include -lhts
|
||||||
|
|
||||||
|
|
||||||
|
htslib/version.h :
|
||||||
|
--- trinityrnaseq.orig/util/misc/bam_gene_tests/write_trin_cmds.pl
|
||||||
|
+++ trinityrnaseq/util/misc/bam_gene_tests/write_trin_cmds.pl
|
||||||
|
@@ -23,7 +23,7 @@
|
||||||
|
|
||||||
|
# Example:
|
||||||
|
#
|
||||||
|
-# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar ~/SVN/trinityrnaseq/trunk/Butterfly/Butterfly.jar --JM 1G --seqType fa
|
||||||
|
+# write_trin_cmds.pl --reads_list_file ReadPartitions.listing --out_token origbfly --SS_lib_type F --full_cleanup_ET --CPU 1 --bfly_jar /usr/share/java/Butterfly.jar --JM 1G --seqType fa
|
||||||
|
|
||||||
|
|
||||||
|
__EOUSAGE__
|
||||||
|
--- trinityrnaseq.orig/util/misc/compare_bflies.pl
|
||||||
|
+++ trinityrnaseq/util/misc/compare_bflies.pl
|
||||||
|
@@ -37,7 +37,7 @@
|
||||||
|
my $cmd = "ln -s $comp.reads .; ln -s $comp.out .";
|
||||||
|
&process_cmd($cmd);
|
||||||
|
|
||||||
|
- $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/prev_vers/Butterfly_r2013_08_14.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
|
||||||
|
+ $cmd = "java -Xmx4G -jar $/usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 --max_number_of_paths_per_node=10 -V 15 --stderr 2>&1 | tee log.txt";
|
||||||
|
|
||||||
|
open (my $ofh, ">bfly.cmd") or die $!;
|
||||||
|
print $ofh $cmd;
|
||||||
|
@@ -61,7 +61,7 @@
|
||||||
|
&process_cmd($cmd);
|
||||||
|
|
||||||
|
|
||||||
|
- $cmd = "java -Xmx4G -jar $TRINITY_HOME/Butterfly/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
|
||||||
|
+ $cmd = "java -Xmx4G -jar /usr/share/java/Butterfly.jar -N 100000 -L 200 -F 500 -C " . basename($comp) . " --path_reinforcement_distance=75 -V 15 --stderr 2>&1 | tee log.txt";
|
||||||
|
|
||||||
|
open (my $ofh, ">bfly.cmd") or die $!;
|
||||||
|
print $ofh $cmd;
|
||||||
|
--- trinityrnaseq.orig/util/misc/sim_test_framework/run_Trinity_eval.pl
|
||||||
|
+++ trinityrnaseq/util/misc/sim_test_framework/run_Trinity_eval.pl
|
||||||
|
@@ -17,7 +17,7 @@
|
||||||
|
|
||||||
|
my $help_flag;
|
||||||
|
my $ref_trans_fa;
|
||||||
|
-my $BFLY_JAR = "$ENV{TRINITY_HOME}/Butterfly/Butterfly.jar";
|
||||||
|
+my $BFLY_JAR = "/usr/share/java/Butterfly.jar";
|
||||||
|
my $INCLUDE_REF_TRANS = 0;
|
||||||
|
my $OUT_DIR = "testing_dir";
|
||||||
|
my $MIN_CONTIG_LENGTH = 200;
|
||||||
|
|
||||||
2814
BioArchLinux/trinityrnaseq/fix_syspath.patch
Normal file
2814
BioArchLinux/trinityrnaseq/fix_syspath.patch
Normal file
File diff suppressed because it is too large
Load diff
16
BioArchLinux/trinityrnaseq/fix_syspath2.patch
Normal file
16
BioArchLinux/trinityrnaseq/fix_syspath2.patch
Normal file
|
|
@ -0,0 +1,16 @@
|
||||||
|
Author: Michael R. Crusoe <crusoe@debian.org>
|
||||||
|
Description: Match the Debian's path
|
||||||
|
Forwarded: not-needed
|
||||||
|
--- a/Trinity
|
||||||
|
+++ b/Trinity
|
||||||
|
@@ -56,8 +56,8 @@ if ($ENV{TRINITY_NO_RETRIES}) {
|
||||||
|
$PARAFLY .= " -max_retry 1 ";
|
||||||
|
}
|
||||||
|
|
||||||
|
-my $TRIMMOMATIC = "$ROOTDIR/trinity-plugins/Trimmomatic/trimmomatic.jar";
|
||||||
|
-my $TRIMMOMATIC_DIR = "$ROOTDIR/trinity-plugins/Trimmomatic";
|
||||||
|
+my $TRIMMOMATIC = "/usr/share/java/trimmomatic/trimmomatic.jar";
|
||||||
|
+my $TRIMMOMATIC_DIR = "/usr/share/java/trimmomatic/";
|
||||||
|
|
||||||
|
$ENV{PATH} = "$ROOTDIR/trinity-plugins/BIN:$ENV{PATH}";
|
||||||
|
|
||||||
|
|
@ -13,3 +13,9 @@ update_on:
|
||||||
use_max_tag: true
|
use_max_tag: true
|
||||||
include_regex: Trinity-v(\d+.\d+.\d+)
|
include_regex: Trinity-v(\d+.\d+.\d+)
|
||||||
prefix: 'Trinity-v'
|
prefix: 'Trinity-v'
|
||||||
|
repo_depends:
|
||||||
|
- parafly
|
||||||
|
- samtools
|
||||||
|
- jellyfish
|
||||||
|
- bowtie2
|
||||||
|
- salmon
|
||||||
|
|
|
||||||
501
BioArchLinux/trinityrnaseq/list
Normal file
501
BioArchLinux/trinityrnaseq/list
Normal file
|
|
@ -0,0 +1,501 @@
|
||||||
|
Analysis/DifferentialExpression/DE_graph_to_dot.pl
|
||||||
|
Analysis/DifferentialExpression/DTE_to_DTU.pl
|
||||||
|
Analysis/DifferentialExpression/GOplot.Rscript
|
||||||
|
Analysis/DifferentialExpression/Glimma.Trinity.Rscript
|
||||||
|
Analysis/DifferentialExpression/PtR
|
||||||
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Analysis/DifferentialExpression/ROKU.pl
|
||||||
|
Analysis/DifferentialExpression/add_annot_to_trans_id.pl
|
||||||
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Analysis/DifferentialExpression/add_annotations_to_GO_and_lengths_file.R
|
||||||
|
Analysis/DifferentialExpression/add_blastx_hit_to_trinity_id.pl
|
||||||
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Analysis/DifferentialExpression/analyze_diff_expr.pl
|
||||||
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Analysis/DifferentialExpression/assign_tissue_specific.pl
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||||||
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Analysis/DifferentialExpression/compare_gene_trans_DE_ranks.pl
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||||||
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Analysis/DifferentialExpression/cut_tree_into_clusters.pl
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||||||
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Analysis/DifferentialExpression/define_clusters_by_cutting_tree.pl
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||||||
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Analysis/DifferentialExpression/diff_expr_analysis_to_heatmap_html.pl
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||||||
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Analysis/DifferentialExpression/diff_express.cgi
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||||||
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Analysis/DifferentialExpression/downsample_count_matrix.pl
|
||||||
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Analysis/DifferentialExpression/extract_GO_enriched_genes.pl
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||||||
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Analysis/DifferentialExpression/filter_diff_expr.pl
|
||||||
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Analysis/DifferentialExpression/filter_matrix_min_sum_rowcounts.pl
|
||||||
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Analysis/DifferentialExpression/get_tissue_enriched_DE_one_vs_all.pl
|
||||||
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Analysis/DifferentialExpression/get_transcript_lengths.pl
|
||||||
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Analysis/DifferentialExpression/identify_diff_isoform_splicing.pl
|
||||||
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Analysis/DifferentialExpression/log2_transform_matrix.pl
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||||||
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Analysis/DifferentialExpression/log2_transform_median_center_fpkm_matrix.pl
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||||||
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Analysis/DifferentialExpression/matrix_to_gene_plots.pl
|
||||||
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Analysis/DifferentialExpression/merge_matrices.pl
|
||||||
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Analysis/DifferentialExpression/merge_subclusters.pl
|
||||||
|
Analysis/DifferentialExpression/plot_all_DE_MAplots.Rscript
|
||||||
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Analysis/DifferentialExpression/plot_all_DE_volcanos.Rscript
|
||||||
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Analysis/DifferentialExpression/plot_expression_patterns.pl
|
||||||
|
Analysis/DifferentialExpression/plot_log2FC_hist.Rscript
|
||||||
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Analysis/DifferentialExpression/prep_n_run_GOplot.pl
|
||||||
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Analysis/DifferentialExpression/prune_isoforms_fasta.pl
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||||||
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Analysis/DifferentialExpression/prune_isoforms_gtf.pl
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||||||
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Analysis/DifferentialExpression/rank_roku_by_expr.pl
|
||||||
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Analysis/DifferentialExpression/remove_batch_effects_from_count_matrix.pl
|
||||||
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Analysis/DifferentialExpression/rename_matrix_column_labels.pl
|
||||||
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Analysis/DifferentialExpression/rename_matrix_feature_identifiers.pl
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||||||
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Analysis/DifferentialExpression/replicates_to_sample_averages_matrix.pl
|
||||||
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Analysis/DifferentialExpression/run_DE_analysis.pl
|
||||||
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Analysis/DifferentialExpression/run_GOseq.pl
|
||||||
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Analysis/DifferentialExpression/run_TMM_normalization_write_FPKM_matrix.pl
|
||||||
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Analysis/DifferentialExpression/stratify_diff_expression.pl
|
||||||
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Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.make_index_html.pl
|
||||||
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Analysis/DifferentialExpression/subcluster_to_canvasXpress_html.pl
|
||||||
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Analysis/DifferentialExpression/summarize_diff_expr_across_min_threshold_ranges.pl
|
||||||
|
Analysis/DifferentialExpression/validate_UP_subset.Rscript
|
||||||
|
Analysis/DifferentialExpression/R/edgeR.TMM.minimal.R
|
||||||
|
Analysis/DifferentialExpression/R/edgeR_funcs.R
|
||||||
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Analysis/DifferentialExpression/R/get_cluster_info.R
|
||||||
|
Analysis/DifferentialExpression/R/heatmap.3.R
|
||||||
|
Analysis/DifferentialExpression/R/jaccard_distance.R
|
||||||
|
Analysis/DifferentialExpression/R/manually_define_clusters.R
|
||||||
|
Analysis/DifferentialExpression/R/misc_rnaseq_funcs.R
|
||||||
|
Analysis/DifferentialExpression/R/pairs3.R
|
||||||
|
Analysis/DifferentialExpression/R/rnaseq_plot_funcs.R
|
||||||
|
Analysis/DifferentialExpression/R/test.heatmap.3.R
|
||||||
|
Analysis/DifferentialExpression/R/vioplot2.R
|
||||||
|
Analysis/DifferentialExpression/R/tests/test_heatmap_w_pca.R
|
||||||
|
Analysis/DifferentialExpression/TissueEnrichment/DE_graph_to_dot.pl
|
||||||
|
Analysis/DifferentialExpression/TissueEnrichment/DE_results_to_pairwise_summary.pl
|
||||||
|
Analysis/DifferentialExpression/TissueEnrichment/README.md
|
||||||
|
Analysis/DifferentialExpression/TissueEnrichment/group_isoforms_by_tissue_enrichment.pl
|
||||||
|
Analysis/DifferentialExpression/TissueEnrichment/pairwise_DE_summary_to_DE_classification.pl
|
||||||
|
Analysis/DifferentialExpression/cluster_sample_data/MLF_ESC_NPC.cuff.genes.fpkm.matrix.gz
|
||||||
|
Analysis/DifferentialExpression/cluster_sample_data/cleanme.pl
|
||||||
|
Analysis/DifferentialExpression/cluster_sample_data/orig.samples.txt
|
||||||
|
Analysis/DifferentialExpression/cluster_sample_data/runMe.sh
|
||||||
|
Analysis/DifferentialExpression/cluster_sample_data/samples.txt
|
||||||
|
Analysis/DifferentialExpression/cluster_sample_data/Islam_scde_data/es.mef.fpkm.matrix
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/DE_pair_counts_to_matrix.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/EBSeq_to_pairwise_summary.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/add_counts_to_classes.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/class_to_separate_fpkm_matrices.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/edgeR_to_pairwise_summary.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/examine_rank_correlation.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/extract_venn_agree_from_summaries.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/mmdiff_to_pairwise_summary.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/notes
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/pairwise_DE_summary_to_DE_classification.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pair_stats.pl
|
||||||
|
Analysis/DifferentialExpression/pairwise_summaries/venn_pairwise_summaries.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/compute_oracle.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/count_by_expression_quintile.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/fusion_comparisons_via_maps_files.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/get_genes_from_maps_file.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/maps_file_to_paralog_representation.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/oracle_counter.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/tier_gene_trans_alignments.tiers_to_boxplot.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/R/boot.tree.R
|
||||||
|
Analysis/FL_reconstruction_analysis/util/blat_full_length_mappings.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/util/blat_map_filter_with_isoforms.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/util/blat_psl_to_align_summary_stats.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/util/blat_query_top_hit_extractor.pl
|
||||||
|
Analysis/FL_reconstruction_analysis/util/blat_top_tier_genes.pl
|
||||||
|
Analysis/SuperTranscripts/README.md
|
||||||
|
Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py
|
||||||
|
Analysis/SuperTranscripts/extract_supertranscript_from_reference.py
|
||||||
|
Analysis/SuperTranscripts/AllelicVariants/VCF_to_annotated_SNP_report.pl
|
||||||
|
Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py
|
||||||
|
Analysis/SuperTranscripts/AllelicVariants/util/clean_bam.pl
|
||||||
|
Analysis/SuperTranscripts/DTU/README.md
|
||||||
|
Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl
|
||||||
|
Analysis/SuperTranscripts/DTU/util/reformat_featureCounts.pl
|
||||||
|
Analysis/SuperTranscripts/_misc/aln_before_after.pl
|
||||||
|
Analysis/SuperTranscripts/pylib/Compact_graph_partial.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Compact_graph_pruner.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Compact_graph_whole.py
|
||||||
|
Analysis/SuperTranscripts/pylib/DP_matrix.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Gene_splice_modeler.py
|
||||||
|
Analysis/SuperTranscripts/pylib/GraphCycleException.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Node_alignment.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Node_path.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Splice_model_refiner.py
|
||||||
|
Analysis/SuperTranscripts/pylib/TGLOBALS.py
|
||||||
|
Analysis/SuperTranscripts/pylib/TGraph.py
|
||||||
|
Analysis/SuperTranscripts/pylib/TNode.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Topological_sort.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Trinity_fasta_parser.py
|
||||||
|
Analysis/SuperTranscripts/pylib/Trinity_util.py
|
||||||
|
Analysis/SuperTranscripts/pylib/__init__.py
|
||||||
|
PerlLib/Ascii_genome_illustrator.pm
|
||||||
|
PerlLib/BED_utils.pm
|
||||||
|
PerlLib/BHStats.pm
|
||||||
|
PerlLib/CIGAR.pm
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PerlLib/CMD_processor.pm
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PerlLib/COMMON.pm
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PerlLib/ColorGradient.pm
|
||||||
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PerlLib/DelimParser.pm
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PerlLib/EM.pm
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PerlLib/Exons_to_geneobj.pm
|
||||||
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PerlLib/Fasta_reader.pm
|
||||||
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PerlLib/Fasta_retriever.pm
|
||||||
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PerlLib/Fastq_reader.pm
|
||||||
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PerlLib/GFF3_alignment_utils.pm
|
||||||
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PerlLib/GFF3_utils.pm
|
||||||
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PerlLib/GFF_maker.pm
|
||||||
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PerlLib/GTF.pm
|
||||||
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PerlLib/GTF_utils.pm
|
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PerlLib/Gene_obj.pm
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PerlLib/Gene_obj_indexer.pm
|
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PerlLib/Longest_orf.pm
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|
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PerlLib/Overlap_info.pm
|
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PerlLib/Overlap_piler.pm
|
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PerlLib/PSL_parser.pm
|
||||||
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PerlLib/Pipeliner.pm
|
||||||
|
PerlLib/Process_cmd.pm
|
||||||
|
PerlLib/SAM_entry.pm
|
||||||
|
PerlLib/SAM_reader.pm
|
||||||
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PerlLib/SingleLinkageClusterer.pm
|
||||||
|
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|
||||||
|
PerlLib/TiedHash.pm
|
||||||
|
PerlLib/VCF_parser.pm
|
||||||
|
PerlLib/WigParser.pm
|
||||||
|
PerlLib/overlapping_nucs.ph
|
||||||
|
PerlLib/test_Fasta_retriever.pl
|
||||||
|
PerlLib/test_htc_gridrunner_LSF.pl
|
||||||
|
PerlLib/test_htc_gridrunner_SGE.pl
|
||||||
|
PerlLib/CDNA/Alignment_segment.pm
|
||||||
|
PerlLib/CDNA/Alternative_splice_comparer.pm
|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
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|
||||||
|
PerlLib/CDNA/Overlap_assembler.pm
|
||||||
|
PerlLib/CDNA/PASA_alignment_assembler.pm
|
||||||
|
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|
||||||
|
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|
||||||
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|
||||||
|
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
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|
||||||
|
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|
||||||
|
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|
||||||
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|
||||||
|
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|
||||||
|
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|
||||||
|
PerlLib/KmerGraphLib/StringNode.pm
|
||||||
|
PerlLib/Simulate/Uniform_Read_Generator.pm
|
||||||
|
PyLib/Pipeliner.py
|
||||||
|
trinity-plugins/BIN/seqtk-trinity
|
||||||
|
trinity-plugins/COLLECTL/examine_resource_usage_profiling.pl
|
||||||
|
trinity-plugins/COLLECTL/util/collectl_dat_to_time_matrix.py
|
||||||
|
trinity-plugins/COLLECTL/util/plot_time_vs_resource.Rscript
|
||||||
|
trinity-plugins/DEXseq_util/dexseq_prepare_annotation.py
|
||||||
|
trinity-plugins/bamsifter/bamsifter
|
||||||
|
trinity-plugins/scaffold_iworm_contigs/scaffold_iworm_contigs
|
||||||
|
trinity-plugins/slclust/bin/slclust
|
||||||
|
util/TrinityStats.pl
|
||||||
|
util/abundance_estimates_to_matrix.pl
|
||||||
|
util/align_and_estimate_abundance.pl
|
||||||
|
util/analyze_blastPlus_topHit_coverage.pl
|
||||||
|
util/filter_low_expr_transcripts.pl
|
||||||
|
util/insilico_read_normalization.pl
|
||||||
|
util/retrieve_sequences_from_fasta.pl
|
||||||
|
util/sift_bam_max_cov.pl
|
||||||
|
util/PBS/N50stats.pl
|
||||||
|
util/PBS/README
|
||||||
|
util/PBS/TRINITY.CONFIG.template
|
||||||
|
util/PBS/pbs_check.pl
|
||||||
|
util/PBS/trinity_kill.pl
|
||||||
|
util/PBS/trinity_kill.sh
|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
|
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|
||||||
|
util/PBS/trinity_pbs.sh
|
||||||
|
util/R/expression_analysis_lib.R
|
||||||
|
util/R/get_Poisson_conf_intervals.R
|
||||||
|
util/misc/ButterflyFastaToGraphDot.pl
|
||||||
|
util/misc/HiCpipe_nameSortedSam_to_raw.pl
|
||||||
|
util/misc/Monarch
|
||||||
|
util/misc/N50.pl
|
||||||
|
util/misc/SAM_coordsorted_max_reads_per_position.pl
|
||||||
|
util/misc/SAM_intron_extractor.pl
|
||||||
|
util/misc/SAM_nameSorted_to_uniq_count_stats.pl
|
||||||
|
util/misc/SAM_pair_to_bed.pl
|
||||||
|
util/misc/SAM_show_alignment.pl
|
||||||
|
util/misc/SAM_show_alignment.summarize_stats.pl
|
||||||
|
util/misc/SAM_sortAny_to_count_stats.pl
|
||||||
|
util/misc/SAM_toString.pl
|
||||||
|
util/misc/SAM_to_bed.pl
|
||||||
|
util/misc/SAM_to_fasta.pl
|
||||||
|
util/misc/SRA_to_fastq.notes
|
||||||
|
util/misc/SRA_to_fastq.pl
|
||||||
|
util/misc/TPM_weighted_gene_length.py
|
||||||
|
util/misc/TophatCufflinksWrapper.pl
|
||||||
|
util/misc/Trinity_genome_aligned_gff3_to_regrouped_genes_gtf.pl
|
||||||
|
util/misc/acc_list_to_fasta_entries.pl
|
||||||
|
util/misc/alexie_analyze_blast.pl
|
||||||
|
util/misc/align_reads_launch_igv.pl
|
||||||
|
util/misc/allele_simulator.pl
|
||||||
|
util/misc/analyze_blastPlus_topHit_coverage.annotate_details_w_FL_info.pl
|
||||||
|
util/misc/analyze_blastPlus_topHit_coverage.by_prioritized_compreh_category.pl
|
||||||
|
util/misc/analyze_blastPlus_topHit_coverage.extract_OS.pl
|
||||||
|
util/misc/analyze_blastPlus_topHit_coverage.org_matrix.pl
|
||||||
|
util/misc/average.pl
|
||||||
|
util/misc/blast_outfmt6_group_segments.pl
|
||||||
|
util/misc/blast_outfmt6_group_segments.to_Markov_Clustering.pl
|
||||||
|
util/misc/blast_outfmt6_group_segments.tophit_coverage.pl
|
||||||
|
util/misc/blastn_wrapper.pl
|
||||||
|
util/misc/capture_orig_n_unmapped_reads.pl
|
||||||
|
util/misc/cat_require_newlines.pl
|
||||||
|
util/misc/cdhit_examine_isoforms.pl
|
||||||
|
util/misc/cdna_fasta_file_to_transcript_gtf.pl
|
||||||
|
util/misc/check_chrysalis_graph_reciprocal_edges.pl
|
||||||
|
util/misc/check_fastQ_pair_ordering.pl
|
||||||
|
util/misc/chrys_graph_to_dot.pl
|
||||||
|
util/misc/collate_fqs.pl
|
||||||
|
util/misc/combined_nameSorted_to_dup_pairs_removed.pl
|
||||||
|
util/misc/compare_FL_stats.pl
|
||||||
|
util/misc/compare_bflies.pl
|
||||||
|
util/misc/component_to_graph_dot.pl
|
||||||
|
util/misc/contig_ExN50_statistic.pl
|
||||||
|
util/misc/convert_fasta_identifiers_for_FL_analysis.pl
|
||||||
|
util/misc/count_N50_given_MIN_FPKM_threshold.pl
|
||||||
|
util/misc/count_features_given_MIN_FPKM_threshold.pl
|
||||||
|
util/misc/count_iso_per_gene_dist.pl
|
||||||
|
util/misc/count_matrix_features_given_MIN_TPM_threshold.pl
|
||||||
|
util/misc/count_number_fasta_seqs.pl
|
||||||
|
util/misc/count_trans_per_component.pl
|
||||||
|
util/misc/decode_SAM_flag_value.pl
|
||||||
|
util/misc/describe_SAM_read_flag_info.pl
|
||||||
|
util/misc/determine_RF_strand_specificity.pl
|
||||||
|
util/misc/ensure_paired_end_bam_file.pl
|
||||||
|
util/misc/examine_iworm_FL_across_threads.pl
|
||||||
|
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|
||||||
|
util/misc/examine_weldmer_halves.pl
|
||||||
|
util/misc/extract_fastQ_pairings.pl
|
||||||
|
util/misc/fan_out_fasta_seqs_to_indiv_files.pl
|
||||||
|
util/misc/fastQ_append_acc.pl
|
||||||
|
util/misc/fastQ_rand_subset.SE.reservoir_sampling_reqiures_high_mem.pl
|
||||||
|
util/misc/fastQ_rand_subset.pl
|
||||||
|
util/misc/fastQ_rand_subset.reservoir_sampling_reqiures_high_mem.pl
|
||||||
|
util/misc/fastQ_top_N_records.pl
|
||||||
|
util/misc/fasta_file_reformatter.pl
|
||||||
|
util/misc/fasta_filter_by_min_length.pl
|
||||||
|
util/misc/fasta_remove_duplicates.pl
|
||||||
|
util/misc/fasta_seq_length.pl
|
||||||
|
util/misc/fasta_to_cmd_generator.pl
|
||||||
|
util/misc/fasta_write_sense_n_anti.pl
|
||||||
|
util/misc/fastq_cleaner.pl
|
||||||
|
util/misc/fastq_interleave_pairs.pl
|
||||||
|
util/misc/fastq_merge_sorted_tab_lists.pl
|
||||||
|
util/misc/fastq_stats.pl
|
||||||
|
util/misc/fastq_unweave_pairs.pl
|
||||||
|
util/misc/filter_out_accs_from_fasta.pl
|
||||||
|
util/misc/filter_similar_seqs_expr_and_strand_aware.pl
|
||||||
|
util/misc/flattened_gff_n_genome_to_Trinity_emulator.pl
|
||||||
|
util/misc/frag_boundary_to_wig.pl
|
||||||
|
util/misc/frag_to_bed.pl
|
||||||
|
util/misc/gene_gff3_to_introns.pl
|
||||||
|
util/misc/gene_to_shared_transcript_content.pl
|
||||||
|
util/misc/genome_gff3_to_gene_gff3_partitions.pl
|
||||||
|
util/misc/get_GC_content_dist.pl
|
||||||
|
util/misc/get_longest_isoform_seq_per_trinity_gene.pl
|
||||||
|
util/misc/get_path_nodes_from_fasta.pl
|
||||||
|
util/misc/get_welds_from_chrysals_graphFromFasta_out.pl
|
||||||
|
util/misc/gff3_file_to_cdna.pl
|
||||||
|
util/misc/gff3_file_utr_coverage_trimmer.pl
|
||||||
|
util/misc/gff3_to_genome_feature_base_encoding.parse_SAM.pl
|
||||||
|
util/misc/gff3_to_genome_feature_base_encoding.pl
|
||||||
|
util/misc/gmap_gff3_chimera_jaccard_analyzer.pl
|
||||||
|
util/misc/gmap_gff3_to_percent_length_stats.count_mapped_transcripts.pl
|
||||||
|
util/misc/gmap_gff3_to_percent_length_stats.pl
|
||||||
|
util/misc/gmap_native_to_format_converter.pl
|
||||||
|
util/misc/gtf_to_bed_format.pl
|
||||||
|
util/misc/gtf_to_introns.pl
|
||||||
|
util/misc/hicpipe_raw_converter.pl
|
||||||
|
util/misc/identify_distal_isoform_variations.pl
|
||||||
|
util/misc/illustrate_ref_comparison.pl
|
||||||
|
util/misc/iworm_welds_to_dot.pl
|
||||||
|
util/misc/jaccard_sam_pair_refiner.pl
|
||||||
|
util/misc/join_any.pl
|
||||||
|
util/misc/join_by_left_col.pl
|
||||||
|
util/misc/join_expr_vals_single_table.pl
|
||||||
|
util/misc/kmer_counter.pl
|
||||||
|
util/misc/m8_blastclust.pl
|
||||||
|
util/misc/map_gtf_transcripts_to_genome_annots.pl
|
||||||
|
util/misc/merge_RSEM_output_to_matrix.pl
|
||||||
|
util/misc/merge_blast_n_rsem_results.pl
|
||||||
|
util/misc/merge_rsem_n_express_for_compare.pl
|
||||||
|
util/misc/mpi_iworm_proc_contigs_to_fa.pl
|
||||||
|
util/misc/nameSorted_SAM_to_FastQ.pl
|
||||||
|
util/misc/nameSorted_SAM_to_paired_fastq.pl
|
||||||
|
util/misc/omp_iworm_thread_contigs_to_fa.pl
|
||||||
|
util/misc/organize_data_table_by_trinity_component.pl
|
||||||
|
util/misc/pair_up_fastq_files_1_2.pl
|
||||||
|
util/misc/pair_up_fastq_files_LeftRight.pl
|
||||||
|
util/misc/pair_up_fastq_files_R1_R2.pl
|
||||||
|
util/misc/pairwise_kmer_content_comparer.pl
|
||||||
|
util/misc/plot_ExN50_statistic.Rscript
|
||||||
|
util/misc/plot_expressed_gene_dist.pl
|
||||||
|
util/misc/plot_strand_specificity_dist_by_quantile.Rscript
|
||||||
|
util/misc/print.pl
|
||||||
|
util/misc/print_kmers.pl
|
||||||
|
util/misc/process_GMAP_alignments_gff3_chimeras_ok.pl
|
||||||
|
util/misc/prop_pair_sam_refiner.pl
|
||||||
|
util/misc/randomly_mutate_seqs.pl
|
||||||
|
util/misc/randomly_sample_PE_fastq.pl
|
||||||
|
util/misc/remove_cntrl_chars.pl
|
||||||
|
util/misc/row_to_column.pl
|
||||||
|
util/misc/run_DETONATE.pl
|
||||||
|
util/misc/run_GSNAP.pl
|
||||||
|
util/misc/run_HISAT.pl
|
||||||
|
util/misc/run_HISAT2_via_samples_file.pl
|
||||||
|
util/misc/run_HiCpipe_bowtie.pl
|
||||||
|
util/misc/run_STAR.pl
|
||||||
|
util/misc/run_STAR_via_samples_file.pl
|
||||||
|
util/misc/run_TOPHAT.pl
|
||||||
|
util/misc/run_bowtie2.pl
|
||||||
|
util/misc/run_bwa.pl
|
||||||
|
util/misc/run_bwasw_trinity.pl
|
||||||
|
util/misc/run_jellyfish.pl
|
||||||
|
util/misc/run_read_simulator_per_fasta_entry.pl
|
||||||
|
util/misc/run_read_simulator_per_gene.pl
|
||||||
|
util/misc/run_trimmomatic_qual_trimming.pl
|
||||||
|
util/misc/seqinfo_refseq_to_dot.pl
|
||||||
|
util/misc/shuffle.pl
|
||||||
|
util/misc/simulate_illuminaPE_from_transcripts.pl
|
||||||
|
util/misc/simulate_illuminaPE_from_transcripts.wgsim.pl
|
||||||
|
util/misc/simulate_reads_sam_and_fa.pl
|
||||||
|
util/misc/sixFrameTranslation.pl
|
||||||
|
util/misc/sort_fastq.pl
|
||||||
|
util/misc/strip_fasta_header.pl
|
||||||
|
util/misc/tab_to_fastQ.pl
|
||||||
|
util/misc/tab_to_fasta.pl
|
||||||
|
util/misc/tblastn_wrapper.pl
|
||||||
|
util/misc/testUnlimitStacksize.pl
|
||||||
|
util/misc/transcript_coverage_UTR_trimmer.pl
|
||||||
|
util/misc/transcript_fasta_to_ORF_pics.pl
|
||||||
|
util/misc/transcript_gff3_to_bed.pl
|
||||||
|
util/misc/transdecoder_pep_to_false_fusion_finder.pl
|
||||||
|
util/misc/trinity_component_distribution.pl
|
||||||
|
util/misc/trinity_trans_matrix_to_rep_trans_gene_matrix.pl
|
||||||
|
util/misc/Artemis/join_multi_wig_to_graph_plot.pl
|
||||||
|
util/misc/Monarch_util/generate_gene_alt_splicing_graphs.pl
|
||||||
|
util/misc/Monarch_util/generate_trans_graphs.pl
|
||||||
|
util/misc/PerlLib/SegmentGraph.pm
|
||||||
|
util/misc/TEST_SUPPORT/BFLY_TESTING/graph_out_to_bfly_cmd.pl
|
||||||
|
util/misc/alt_GG_read_partitioning_JCornish/genwig.sh
|
||||||
|
util/misc/alt_GG_read_partitioning_JCornish/genwig2.py
|
||||||
|
util/misc/altsplice_simulation_toolkit/sim_single_bubble.pl
|
||||||
|
util/misc/bam_gene_tests/extract_bam_reads_per_target_gene.pl
|
||||||
|
util/misc/bam_gene_tests/extract_bam_reads_per_target_transcript.pl
|
||||||
|
util/misc/bam_gene_tests/harvest_transcripts.pl
|
||||||
|
util/misc/bam_gene_tests/write_trin_cmds.pl
|
||||||
|
util/misc/blat_util/blat_sam_add_reads2.pl
|
||||||
|
util/misc/blat_util/blat_to_sam.pl
|
||||||
|
util/misc/blat_util/blat_top_hit_extractor.pl
|
||||||
|
util/misc/blat_util/process_BLAT_alignments.pl
|
||||||
|
util/misc/blat_util/pslx_to_gff3.pl
|
||||||
|
util/misc/blat_util/run_BLAT_shortReads.pl
|
||||||
|
util/misc/blat_util/top_blat_sam_extractor.pl
|
||||||
|
util/misc/insilico_norm_kmer_hists/kmer_histo.NormMaxKCov50.txt
|
||||||
|
util/misc/insilico_norm_kmer_hists/kmer_histo.all.txt
|
||||||
|
util/misc/insilico_norm_kmer_hists/plot_me.R
|
||||||
|
util/misc/insilico_norm_kmer_hists/result.pdf
|
||||||
|
util/misc/iso_reco_analysis/bam_to_cuff.pl
|
||||||
|
util/misc/iso_reco_analysis/cuff_gtf_to_bed.pl
|
||||||
|
util/misc/iso_reco_analysis/gene_gff3_to_bed_cmds.pl
|
||||||
|
util/misc/iso_reco_analysis/gmap_to_ref.pl
|
||||||
|
util/misc/iso_reco_analysis/notes
|
||||||
|
util/misc/iso_reco_analysis/run_trinity_WITH_LR.pl
|
||||||
|
util/misc/iso_reco_analysis/run_trinity_no_LR.pl
|
||||||
|
util/misc/iso_reco_analysis/sim_reads.pl
|
||||||
|
util/misc/iso_reco_analysis/trans_gff3_to_bed_cmds.pl
|
||||||
|
util/misc/sim_test_framework/audit_summary_stats.pl
|
||||||
|
util/misc/sim_test_framework/audit_summary_stats.reexamine.pl
|
||||||
|
util/misc/sim_test_framework/info_files_to_eval_cmds.pl
|
||||||
|
util/misc/sim_test_framework/partition_target_transcripts.pl
|
||||||
|
util/misc/sim_test_framework/run_Trinity_eval.pl
|
||||||
|
util/misc/sim_test_framework/run_Trinity_eval.sh
|
||||||
|
util/misc/sim_test_framework/run_simulate_reads.wgsim.pl
|
||||||
|
util/misc/sim_test_framework/write_simulate_read_commands.pl
|
||||||
|
util/misc/sim_test_framework/util/find_pruned_edges_shouldve_kept.pl
|
||||||
|
util/misc/splice_path_analysis/assess_intron_path_sensitivity.pl
|
||||||
|
util/misc/splice_path_analysis/assess_intron_path_sensitivity.summarizer.pl
|
||||||
|
util/misc/splice_path_analysis/diff_splice_paths.pl
|
||||||
|
util/misc/splice_path_analysis/intron_barcharter.pl
|
||||||
|
util/support_scripts/GG_partitioned_trinity_aggregator.pl
|
||||||
|
util/support_scripts/SAM_coordSorted_fragment_Read_coverage_writer.pl
|
||||||
|
util/support_scripts/SAM_coordSorted_fragment_coverage_writer2.pl
|
||||||
|
util/support_scripts/SAM_extract_properly_mapped_pairs.pl
|
||||||
|
util/support_scripts/SAM_extract_uniquely_mapped_reads.pl
|
||||||
|
util/support_scripts/SAM_filter_out_unmapped_reads.pl
|
||||||
|
util/support_scripts/SAM_ordered_pair_jaccard.pl
|
||||||
|
util/support_scripts/SAM_set_transcribed_orient_info.pl
|
||||||
|
util/support_scripts/SAM_strand_separator.pl
|
||||||
|
util/support_scripts/SAM_to_frag_coords.pl
|
||||||
|
util/support_scripts/add_LR_reads_to_iworm_bundle.pl
|
||||||
|
util/support_scripts/annotate_chrysalis_welds_with_iworm_names.pl
|
||||||
|
util/support_scripts/batch_cmds.pl
|
||||||
|
util/support_scripts/bowtie2_wrapper.pl
|
||||||
|
util/support_scripts/define_SAM_coverage_partitions2.pl
|
||||||
|
util/support_scripts/define_coverage_partitions.pl
|
||||||
|
util/support_scripts/eXpress_trans_to_gene_results.pl
|
||||||
|
util/support_scripts/ensure_coord_sorted_sam.pl
|
||||||
|
util/support_scripts/extract_reads_per_partition.pl
|
||||||
|
util/support_scripts/fastQ_to_fastA.pl
|
||||||
|
util/support_scripts/fastQ_to_tab.pl
|
||||||
|
util/support_scripts/fasta_find_duplicates.pl
|
||||||
|
util/support_scripts/fasta_to_tab.pl
|
||||||
|
util/support_scripts/filter_iworm_by_min_length_or_cov.pl
|
||||||
|
util/support_scripts/filter_transcripts_require_min_cov.pl
|
||||||
|
util/support_scripts/fragment_coverage_writer.pl
|
||||||
|
util/support_scripts/get_Trinity_gene_to_trans_map.pl
|
||||||
|
util/support_scripts/inchworm_transcript_splitter.pl
|
||||||
|
util/support_scripts/iworm_LR_to_scaff_pairs.pl
|
||||||
|
util/support_scripts/jaccard_fasta_clipper.pl
|
||||||
|
util/support_scripts/jaccard_wig_clipper.pl
|
||||||
|
util/support_scripts/join_partitions_within_range.pl
|
||||||
|
util/support_scripts/kallisto_trans_to_gene_results.pl
|
||||||
|
util/support_scripts/merge_pair_and_LR_scaff_links.pl
|
||||||
|
util/support_scripts/nbkc_merge_left_right_stats.pl
|
||||||
|
util/support_scripts/nbkc_normalize.pl
|
||||||
|
util/support_scripts/ordered_fragment_coords_to_jaccard.pl
|
||||||
|
util/support_scripts/outfmt6_add_percent_match_length.pl
|
||||||
|
util/support_scripts/partition_chrysalis_graphs_n_reads.pl
|
||||||
|
util/support_scripts/partitioned_trinity_aggregator.pl
|
||||||
|
util/support_scripts/plugin_install_tests.sh
|
||||||
|
util/support_scripts/prep_rnaseq_alignments_for_genome_assisted_assembly.pl
|
||||||
|
util/support_scripts/print_butterfly_assemblies.pl
|
||||||
|
util/support_scripts/process_GMAP_alignments_gff3_chimeras_ok.pl
|
||||||
|
util/support_scripts/revcomp_fasta.pl
|
||||||
|
util/support_scripts/run_TMM_scale_matrix.pl
|
||||||
|
util/support_scripts/run_UpperQuartileNormalization_matrix.pl
|
||||||
|
util/support_scripts/salmon_runner.pl
|
||||||
|
util/support_scripts/salmon_trans_to_gene_results.pl
|
||||||
|
util/support_scripts/scaffold_iworm_contigs.pl
|
||||||
|
util/support_scripts/segment_GFF_partitions.pl
|
||||||
|
util/support_scripts/trinity_install_tests.sh
|
||||||
|
util/support_scripts/trinity_installer.py
|
||||||
|
util/support_scripts/wig_clip_to_bed.pl
|
||||||
|
util/support_scripts/write_partitioned_trinity_cmds.pl
|
||||||
|
util/support_scripts/tests/sample_data_tests.py
|
||||||
|
util/support_scripts/tests/test_prep.py
|
||||||
|
util/support_scripts/tests/tests.py
|
||||||
|
usr/share/doc/trinityrnaseq/README
|
||||||
|
usr/share/doc/trinityrnaseq/TODO.Debian
|
||||||
|
usr/share/doc/trinityrnaseq/changelog.Debian.gz
|
||||||
|
usr/share/doc/trinityrnaseq/changelog.gz
|
||||||
|
usr/share/doc/trinityrnaseq/copyright
|
||||||
|
usr/share/doc/trinityrnaseq/run-tests
|
||||||
|
usr/share/java/Butterfly-2.11.0.jar
|
||||||
|
usr/share/man/man1/Trinity.1.gz
|
||||||
|
|
@ -1,12 +0,0 @@
|
||||||
diff --git a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
|
|
||||||
index e8ecbcf..ccdbd27 100644
|
|
||||||
--- a/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
|
|
||||||
+++ b/trinity-plugins/bamsifter/sift_bam_max_cov.cpp
|
|
||||||
@@ -10,6 +10,7 @@
|
|
||||||
#include <set>
|
|
||||||
#include <utility>
|
|
||||||
#include <vector>
|
|
||||||
+#include <string>
|
|
||||||
|
|
||||||
#include "htslib/sam.h"
|
|
||||||
#include "htslib/bgzf.h"
|
|
||||||
Loading…
Add table
Reference in a new issue