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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70 |
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modified:
analyze_diff_expr.xml macros.xml test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf test-data/count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf test-data/count/qcheck/wt_37.rep_compare.pdf test-data/count/qcheck/wt_GSNO.rep_compare.pdf test-data/count/qcheck/wt_ph8.rep_compare.pdf test-data/filtered/Trinity_filtered_exp.fasta test-data/filtered/Trinity_filtered_hi_iso.fasta test-data/filtered/Trinity_filtered_pct_iso.fasta |
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| diff -r 3f4094b6a565 -r c0096052b35b analyze_diff_expr.xml --- a/analyze_diff_expr.xml Sun Dec 19 16:21:54 2021 +0000 +++ b/analyze_diff_expr.xml Tue Apr 11 19:55:15 2023 +0000 |
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| b'@@ -1,15 +1,10 @@\n-<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@WRAPPER_VERSION@">\n+<tool id="trinity_analyze_diff_expr" name="Extract and cluster differentially expressed transcripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">\n <description>from a Trinity assembly</description>\n <macros>\n <import>macros.xml</import>\n </macros>\n <expand macro="bio_tools"/>\n- <expand macro="requirements">\n- <requirement type="package" version="2.18.0">bioconductor-qvalue</requirement>\n- <requirement type="package" version="1.36.0">bioconductor-goseq</requirement>\n- <requirement type="package" version="2.0.8">r-cluster</requirement>\n- <requirement type="package" version="1.1.25">r-fastcluster</requirement>\n- </expand>\n+ <expand macro="requirements"/>\n <command detect_errors="aggressive"><![CDATA[\n ## DE results input files must be in the working directory and have suffix .DE_results\n #import re\n@@ -35,8 +30,8 @@\n analyze_diff_expr.pl\n --matrix \'${matrix}\'\n --samples \'${samples}\'\n- -P ${p}\n- -C ${c}\n+ -P ${P}\n+ -C ${C}\n \n #if str( $additional_params.max_DE_genes_per_comparison ):\n --max_DE_genes_per_comparison ${additional_params.max_DE_genes_per_comparison}\n@@ -57,26 +52,26 @@\n --output results\n ]]></command>\n <inputs>\n- <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="Raw counts matrix produced by \'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity\' tool"/>\n- <param format="tabular" name="samples" argument="--samples" type="data" label="Sample description" help="File describing samples and replicates"/>\n- <param format="tabular" name="DE_results" type="data_collection" collection_type="list" label="Differential expression results" help="Generated by \'Differential expression analysis using a Trinity assembly\' tool"/>\n- <param name="p" type="float" argument="-P" value="0.001" label="p-value cutoff for FDR"/>\n- <param name="c" type="float" argument="-C" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>\n+ <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="Raw counts matrix produced by \'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity\' tool"/>\n+ <param argument="--samples" format="tabular" type="data" label="Sample description" help="File describing samples and replicates"/>\n+ <param name="DE_results" format="tabular" type="data_collection" collection_type="list" label="Differential expression results" help="Generated by \'Differential expression analysis using a Trinity assembly\' tool"/>\n+ <param argument="-P" type="float" value="0.001" label="p-value cutoff for FDR"/>\n+ <param argument="-C" type="float" value="2" label="min abs(log2(a/b)) fold change" help="Default: 2 (meaning 2^(2) or 4-fold"/>\n <section name="additional_params" title="Additional Options" expanded="False">\n- <param name="max_DE_genes_per_comparison" argument="--max_DE_genes_per_comparison" type="integer" value="" optional="true" label="Maximum differential expression genes per comparison" help="Extract only up to the top number of DE features within each pairwise comparison. This is useful when you have massive numbers of DE features but still want to make useful heatmaps and other plots with more manageable numbers of data points."/>\n- <param name="order_columns_by_samples_file" argument="--order_columns_by_samples_file" type="boolean" checked="false" truevalue="--order_columns_by_samples_file" falsevalue="" label="Order columns by samples file" help="Instead of clustering samples or replicates hierarchically based on gene expression patterns, order columns acco'..b'mples_file" falsevalue="" label="Order columns by samples file" help="Instead of clustering samples or replicates hierarchically based on gene expression patterns, order columns according to order in the --samples file."/>\n+ <param argument="--max_genes_clust" type="integer" value="10000" label="Maximum genes in cluster" help="If more than 10000, heatmaps are not generated, since too time consuming"/>\n <conditional name="GO_enrichment">\n- <param type="select" name="examine_GO_enrichment" argument="--examine_GO_enrichment" label="Run GO enrichment analysis" help="To examine GO enrichment, you must first run Trinotate and then extract all GO assignments for each gene feature, with the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl">\n+ <param argument="--examine_GO_enrichment" type="select" label="Run GO enrichment analysis" help="To examine GO enrichment, you must first run Trinotate and then extract all GO assignments for each gene feature, with the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl">\n <option value="no">No</option>\n <option value="yes">Yes</option>\n </param>\n <when value="no">\n </when>\n <when value="yes">\n- <param format="tabular" name="DE_matrices" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by \'Differential expression analysis using a Trinity assembly\' tool. If not, be careful that the file names are identical to the file names of differential expression results, with extension \'.count_matrix\' instead of \'.DE_results\'."/>\n- <param format="tabular" name="GO_annots" argument="--GO_annots" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/>\n- <param format="tabular" name="gene_lengths" argument="--gene_lengths" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>\n+ <param name="DE_matrices" format="tabular" type="data_collection" collection_type="list" label="Differential expression count matrices" help="Generated by \'Differential expression analysis using a Trinity assembly\' tool. If not, be careful that the file names are identical to the file names of differential expression results, with extension \'.count_matrix\' instead of \'.DE_results\'."/>\n+ <param argument="--GO_annots" format="tabular" type="data" label="Extracted GO assignments file" help="Generated by the Trinotate script extract_GO_assignments_from_Trinotate_xls.pl. Must have 2 columns: feature_id GO:000001,GO:00002,..."/>\n+ <param argument="--gene_lengths" format="tabular" type="data" label="Gene length file" help="Must have 2 columns: feature_id length"/>\n </when>\n </conditional>\n </section>\n@@ -93,7 +88,7 @@\n <data format="tabular" name="results_matrix_log2_sample_cor" from_work_dir="results.matrix.log2.sample_cor.dat"/>\n <data format="pdf" name="results_matrix_log2_sample_cor_matrix" from_work_dir="results.matrix.log2.sample_cor_matrix.pdf"/>\n </collection>\n- <data format="rdata" name="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/>\n+ <data name="rdata" format="rdata" label="${tool.name} on ${on_string}: RData file" from_work_dir="results.matrix.RData"/>\n <collection name="GOseq_enrichment" type="list" label="${tool.name} on ${on_string}: GOseq enriched and depleted categories">\n <filter>additional_params[\'GO_enrichment\'][\'examine_GO_enrichment\'] == \'yes\'</filter>\n <discover_datasets pattern="(?P<name>.+\\.subset\\.GOseq\\.(enriched|depleted))$" ext="tabular" />\n' |
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| diff -r 3f4094b6a565 -r c0096052b35b macros.xml --- a/macros.xml Sun Dec 19 16:21:54 2021 +0000 +++ b/macros.xml Tue Apr 11 19:55:15 2023 +0000 |
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| @@ -1,8 +1,7 @@ -<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="@WRAPPER_VERSION@">trinity</requirement> + <requirement type="package" version="@TOOL_VERSION@">trinity</requirement> <yield/> </requirements> </xml> @@ -11,10 +10,11 @@ <xref type="bio.tools">trinity</xref> </xrefs> </xml> - <token name="@WRAPPER_VERSION@">2.9.1</token> + <token name="@TOOL_VERSION@">2.15.1</token> + <token name="@VERSION_SUFFIX@">0</token> <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> - #if $pool.inputs.strand.is_strand_specific: + #if $pool.inputs.strand.is_strand_specific == 'true': --SS_lib_type $pool.inputs.strand.library_type #end if @@ -23,7 +23,10 @@ <xml name="input_paired_strand_jaccard"> <conditional name="strand"> - <param name="is_strand_specific" type="boolean" checked="false" label="Strand specific data"/> + <param name="is_strand_specific" type="select" label="Strand specific data"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> <when value="false" /> <when value="true"> <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific library type"> @@ -35,6 +38,22 @@ <param argument="--jaccard_clip" type="boolean" truevalue="--jaccard_clip" falsevalue="" checked="false" label="Jaccard Clip options" help="Set if you expect high gene density with UTR overlap"/> </xml> + <xml name="is_strand_specific_f_r"> + <conditional name="strand"> + <param name="is_strand_specific" type="select" label="Strand specific data"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false"/> + <when value="true"> + <param name="library_type" argument="--SS_lib_type" type="select" label="Strand-specific Library Type"> + <option value="F">F</option> + <option value="R">R</option> + </param> + </when> + </conditional> + </xml> + <xml name="citation"> <citations> <citation type="doi">10.1038/nbt.1883</citation> |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf |
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| Binary file test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf has changed |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix --- a/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix Tue Apr 11 19:55:15 2023 +0000 |
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| @@ -1,7 +1,7 @@ wt_37_2 wt_37_3 wt_37_1 wt_ph8_3 wt_ph8_1 wt_ph8_2 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 +TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 -0.353285722910146 -0.874117886211586 -0.590324920210995 1.12588211378841 1.65760259323259 1.57960008123132 TR24|c0_g1_i1 0.106533882165825 -0.313797916782532 0.025003996669227 1.39963914188743 1.22079106142351 1.25695072471892 -1.19180739240392 -1.23133575659056 -1.2719777410879 -TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 1.74646076035339 1.75438767612502 1.74380874666379 -1.13287411273457 -0.795433018475884 -0.712970858283911 TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.43575453462855 1.4783149968566 1.36038927229391 1.02359379610527 1.32351327005887 1.20686835120661 -TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.98577454287534 1.99158406095747 1.95736061514986 1.41625240401813 1.71671228997234 1.68718414007205 +TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 1.74646076035339 1.75438767612502 1.74380874666379 -1.13287411273457 -0.795433018475884 -0.712970858283911 TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 2.50474970263492 2.07793503557972 2.30706903479522 -2.04544737992556 -1.68287730054085 -1.39337068334587 -TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 -0.353285722910146 -0.874117886211586 -0.590324920210995 1.12588211378841 1.65760259323259 1.57960008123132 +TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.98577454287534 1.99158406095747 1.95736061514986 1.41625240401813 1.71671228997234 1.68718414007205 |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix --- a/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix Tue Apr 11 19:55:15 2023 +0000 |
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| @@ -1,8 +1,8 @@ wt_37_2 wt_37_3 wt_37_1 wt_ph8_3 wt_ph8_1 wt_ph8_2 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 +TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -1.41510217339161 -2.41510217339161 -1.83013967267045 -0.607747251334006 -0.607747251334006 -0.41510217339161 +TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -0.339510283104669 -0.357888812419525 -0.296334141902888 -1.67981690730689 -1.51400801433681 -1.59017969482221 +TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.982236357836205 0.280798047997588 -0.982236357836205 -0.304164452723568 -1.30416445272357 +TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 0.965440325233136 -0.619522175488021 0.0585497296246169 -2.94145027037538 -0.619522175488021 -1.35648776965423 TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.44630436384266 -1.5322044372483 -1.46308007659348 -1.98611482817144 -1.80411699442855 -1.51461037723356 -TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 0.965440325233136 -0.619522175488021 0.0585497296246169 -2.94145027037538 -0.619522175488021 -1.35648776965423 TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.0643684375088904 -1.06436843750889 -1.06436843750889 -0.479405936787734 -2.06436843750889 -1.06436843750889 -TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -1.41510217339161 -2.41510217339161 -1.83013967267045 -0.607747251334006 -0.607747251334006 -0.41510217339161 -TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.982236357836205 0.280798047997588 -0.982236357836205 -0.304164452723568 -1.30416445272357 -TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -0.339510283104669 -0.357888812419525 -0.296334141902888 -1.67981690730689 -1.51400801433681 -1.59017969482221 TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.346801079601032 -1.34680107960103 -1.34680107960103 -0.761838578879876 0.238161421120124 |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Tue Apr 11 19:55:15 2023 +0000 |
| b |
| b'@@ -1,38 +1,38 @@\n sampleA\tsampleB\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR4277|c0_g1_i1\twt_37\twt_GSNO\t3852.97388871986\t161.116814813422\t2007.04535176664\t4.57661492404411\t0.121615845393926\t37.6317321909822\t0\t0\n-TR131|c0_g1_i1\twt_37\twt_GSNO\t26.1866396538608\t1340.30918254958\t683.247911101723\t-5.68565819121436\t0.188173369545147\t-30.2149990987446\t1.50487696827007e-200\t2.48304699764561e-199\n-TR4761|c0_g1_i1\twt_37\twt_GSNO\t1645.20640957447\t193.196157329029\t919.201283451752\t3.09227622940716\t0.143766888218038\t21.5089598706302\t1.28350063536341e-102\t1.41185069889975e-101\n-TR3091|c0_g1_i1\twt_37\twt_GSNO\t16.7444693227929\t328.569936894811\t172.657203108802\t-4.30529554105297\t0.242003292489129\t-17.790235400398\t8.41257542125902e-71\t6.94037472253869e-70\n-TR3638|c0_g1_i1\twt_37\twt_GSNO\t583.00358519031\t183.754416330029\t383.37900076017\t1.66225356244238\t0.144704273829595\t11.487245804501\t1.5290952692426e-30\t1.00920287770012e-29\n-TR2487|c0_g1_i1\twt_37\twt_GSNO\t342.210853400436\t920.407318992504\t631.30908619647\t-1.42823125318501\t0.124766100464837\t-11.44727011475\t2.42667678803784e-30\t1.33467223342081e-29\n-TR3788|c0_g1_i1\twt_37\twt_GSNO\t19.5075441237117\t134.95369713876\t77.2306206312357\t-2.78185518936858\t0.26452057618315\t-10.5165928091827\t7.24461724546031e-26\t3.41531955857415e-25\n-TR1479|c0_g1_i1\twt_37\twt_GSNO\t129.593534475689\t371.064629188207\t250.329081831948\t-1.51632040995179\t0.145721574162902\t-10.405599985193\t2.33778717307793e-25\t9.64337208894648e-25\n-TR2107|c1_g1_i1\twt_37\twt_GSNO\t48.9228907410258\t7.40521775805688\t28.1640542495414\t2.72565745131165\t0.439033221898883\t6.20831708252687\t5.35550100392654e-10\t1.96368370143973e-09\n-TR3854|c0_g1_i1\twt_37\twt_GSNO\t1573.69549271337\t2374.56159860719\t1974.12854566028\t-0.593952181868433\t0.11125243839418\t-5.33877900063632\t9.35746226940931e-08\t3.08796254890507e-07\n-TR2122|c0_g2_i2\twt_37\twt_GSNO\t119.534640490118\t199.143666337033\t159.339153413576\t-0.73989736621081\t0.168946597067547\t-4.37947481070002\t1.18965671308434e-05\t3.56897013925302e-05\n-TR1449|c0_g1_i1\twt_37\twt_GSNO\t180.814952011467\t104.755290736358\t142.785121373912\t0.785811747593425\t0.186397685526418\t4.2157806057203\t2.48915666101662e-05\t6.6882655779165e-05\n-TR4163|c0_g1_i1\twt_37\twt_GSNO\t347.283468916919\t232.772947466212\t290.028208191566\t0.5773903092812\t0.137377906430929\t4.20293425836637\t2.63477128827014e-05\t6.6882655779165e-05\n-TR2672|c0_g1_i1\twt_37\twt_GSNO\t18.3155337236093\t2.26581902751323\t10.2906763755613\t2.9857084616452\t0.761209385049731\t3.92232218924907\t8.76996107235725e-05\t0.000206720510991278\n-TR5055|c0_g2_i1\twt_37\twt_GSNO\t23.3590211688541\t5.52768338415684\t14.4433522765055\t2.08513896568298\t0.577312677901881\t3.61180179389265\t0.00030407694239889\t0.000668969273277559\n-TR2844|c0_g1_i1\twt_37\twt_GSNO\t158.206282615139\t231.762548186068\t194.984415400603\t-0.551426184671915\t0.155135532159318\t-3.55448024702441\t0.000378726959348647\t0.000781124353656584\n-TR127|c1_g1_i1\twt_37\twt_GSNO\t13.461799216177\t1.21881296083961\t7.34030608850831\t3.52517488060096\t1.00261297574214\t3.51598769005717\t0.00043812129728732\t0.000850470753557739\n-TR5212|c0_g1_i1\twt_37\twt_GSNO\t65.7079302129484\t107.875371765755\t86.7916509893515\t-0.715754705745061\t0.210644233010842\t-3.39793164766215\t0.000678973819799399\t0.0012447853362989\n-TR1894|c2_g1_i1\twt_37\twt_GSNO\t13.3497721959996\t2.96749216411516\t8.15863218005739\t2.116499695166\t0.744618031030184\t2.84239651333424\t0.00447757649596373\t0.00777684338772647\n-TR24|c0_g1_i1\twt_37\twt_GSNO\t69.9065207344592\t41.2394742844514\t55.5729975094553\t0.763675526543044\t0.270944643994893\t2.81856660933825\t0.00482386011442888\t0.00795936918880766\n+TR4277|c0_g1_i1\twt_37\twt_GSNO\t3852.97388871986\t161.116814813422\t2007.04535176664\t4.57661492404411\t0.121615845393921\t37.6317321909836\t0\t0\n+TR131|c0_g1_i1\twt_37\twt_GSNO\t26.1866396538608\t1340.30918254958\t683.247911101723\t-5.68565819121436\t0.188173369545145\t-30.214999098745\t1.5048769682518e-200\t2.48304699761546e-199\n+TR4761|c0_g1_i1\twt_37\twt_GSNO\t1645.20640957447\t193.196157329029\t919.201283451752\t3.09227622940716\t0.14376'..b'3018853512\t9.23822794034992\t12.5507649128506\t0.776103293030194\t0.516446682273215\t1.5027752518693\t0.13289700980576\t0.16070937436521\n-TR4859|c0_g1_i1\twt_37\twt_GSNO\t7.32690480813971\t3.17910584569163\t5.25300532691567\t1.23041974278822\t0.82607009598701\t1.48948587869905\t0.13635946915836\t0.16070937436521\n-TR939|c0_g1_i1\twt_37\twt_GSNO\t84.2568220960088\t96.9171174594069\t90.5869697777078\t-0.203187486812458\t0.203052234052517\t-1.00066609835923\t0.316988262617008\t0.354139456794138\n-TR2278|c0_g1_i1\twt_37\twt_GSNO\t486.5272515724\t448.140178813055\t467.333715192727\t0.118924512672215\t0.120068895863502\t0.990468945491189\t0.321944960721944\t0.354139456794138\n-TR2011|c5_g1_i1\twt_37\twt_GSNO\t5.60408627995835\t7.88255079488408\t6.74331853742122\t-0.50342873702063\t0.712267625142964\t-0.706797163383052\t0.479692537619295\t0.510640443272153\n-TR2182|c3_g2_i6\twt_37\twt_GSNO\t2.24974854180929\t1.3031439398571\t1.77644624083319\t0.878491642458712\t1.45214866443311\t0.604959852923637\t0.545205672528741\t0.562243349795264\n+TR2779|c0_g1_i1\twt_37\twt_GSNO\t155.915506826481\t205.619872596257\t180.767689711369\t-0.403209397282847\t0.189507562454757\t-2.12766916559918\t0.0333645231630914\t0.0500467847446371\n+TR3807|c0_g1_i1\twt_37\twt_GSNO\t3.48709246029019\t0.350050334268211\t1.9185713972792\t3.04810928058763\t1.5874506366217\t1.92012854464212\t0.054841664536056\t0.0786858665082543\n+TR1492|c0_g1_i2\twt_37\twt_GSNO\t1640.89375005483\t1435.64893261411\t1538.27134133447\t0.192601921423702\t0.101311986688034\t1.90107733270273\t0.0572918841322478\t0.0787763406818408\n+TR4084|c0_g1_i1\twt_37\twt_GSNO\t93.2264707954139\t121.352438036668\t107.289454416041\t-0.381231151484283\t0.213992488133209\t-1.78151651401413\t0.0748281095286238\t0.0987731045777834\n+TR1891|c0_g1_i1\twt_37\twt_GSNO\t107.628573623499\t135.399287466928\t121.513930545214\t-0.329513668205707\t0.189733845104182\t-1.73671528147639\t0.0824374390602302\t0.104632134191831\n+TR1837|c2_g1_i1\twt_37\twt_GSNO\t0.308903905435236\t2.22601224010275\t1.26745807276899\t-2.87715913917267\t1.7927876855897\t-1.60485213184978\t0.108526350064413\t1\n+TR5075|c0_g1_i1\twt_37\twt_GSNO\t15.8633018853512\t9.23822794034992\t12.5507649128506\t0.776103293030194\t0.516446682273216\t1.5027752518693\t0.132897009805761\t0.160709374365211\n+TR4859|c0_g1_i1\twt_37\twt_GSNO\t7.32690480813971\t3.17910584569163\t5.25300532691567\t1.23041974278822\t0.82607009598701\t1.48948587869905\t0.136359469158361\t0.160709374365211\n+TR939|c0_g1_i1\twt_37\twt_GSNO\t84.2568220960088\t96.9171174594069\t90.5869697777078\t-0.203187486812456\t0.203052234052516\t-1.00066609835922\t0.316988262617012\t0.35413945679411\n+TR2278|c0_g1_i1\twt_37\twt_GSNO\t486.5272515724\t448.140178813055\t467.333715192727\t0.118924512672213\t0.120068895863495\t0.990468945491242\t0.321944960721918\t0.35413945679411\n+TR2011|c5_g1_i1\twt_37\twt_GSNO\t5.60408627995835\t7.88255079488408\t6.74331853742122\t-0.503428737020628\t0.712267625142964\t-0.70679716338305\t0.479692537619297\t0.510640443272154\n+TR2182|c3_g2_i6\twt_37\twt_GSNO\t2.24974854180929\t1.3031439398571\t1.77644624083319\t0.878491642458711\t1.45214866443311\t0.604959852923636\t0.545205672528742\t0.562243349795265\n TR3249|c0_g1_i1\twt_37\twt_GSNO\t1.12573841927462\t2.128954842887\t1.62734663108081\t-0.858277190977929\t1.45820967054459\t-0.588582841216099\t0.556141147160533\t1\n TR1678|c0_g1_i1\twt_37\twt_GSNO\t0.595141051681226\t0.700100668536423\t0.647620860108824\t-0.322353878735801\t2.26929239960538\t-0.142050393678601\t0.887040200834538\t1\n-TR1122|c0_g1_i1\twt_37\twt_GSNO\t1.41370386226057\t1.3031439398571\t1.35842390105883\t0.189589394350501\t1.67633508161709\t0.113097552171736\t0.909953215626095\t1\n-TR1982|c2_g1_i1\twt_37\twt_GSNO\t5.73684100209948\t5.71221669652109\t5.72452884931028\t-0.0104554076697487\t0.738553450989727\t-0.0141566025529196\t0.988705042660126\t0.988705042660126\n+TR1122|c0_g1_i1\twt_37\twt_GSNO\t1.41370386226057\t1.3031439398571\t1.35842390105883\t0.1895893943505\t1.67633508161709\t0.113097552171736\t0.909953215626095\t1\n+TR1982|c2_g1_i1\twt_37\twt_GSNO\t5.73684100209948\t5.71221669652109\t5.72452884931028\t-0.0104554076697489\t0.738553450989728\t-0.0141566025529198\t0.988705042660126\t0.988705042660126\n' |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf |
| b |
| Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Tue Apr 11 19:55:15 2023 +0000 |
| b |
| @@ -1,38 +1,38 @@ sampleA sampleB logFC logCPM PValue FDR -TR131|c0_g1_i1 wt_37 wt_GSNO -5.83641794955382 16.0393491449056 0 0 -TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41329536892161 17.453649857324 0 0 -TR3091|c0_g1_i1 wt_37 wt_GSNO -4.45192710783926 14.0403115023365 4.66239713643175e-192 5.75028980159916e-191 -TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92754337500687 16.3361488759619 3.05265683396309e-191 2.82370757141586e-190 -TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58705168340508 15.8893887856701 9.57106937146597e-124 7.08259133488482e-123 -TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67065982572176 14.5610246448295 4.39649357092684e-84 2.71117103540489e-83 -TR3638|c0_g1_i1 wt_37 wt_GSNO 1.49937182627392 15.1071990563814 1.60652562072048e-64 8.49163542380826e-64 -TR3854|c0_g1_i1 wt_37 wt_GSNO -0.756864683109858 17.5153338325952 9.14141417630157e-40 4.22790405653948e-39 -TR2122|c0_g2_i2 wt_37 wt_GSNO -0.90394318029981 13.8984589155106 3.98287653266084e-13 1.63740479676057e-12 -TR2844|c0_g1_i1 wt_37 wt_GSNO -0.707834005847516 14.1849675326065 1.90004997002049e-12 7.0301848890758e-12 -TR3788|c0_g1_i1 wt_37 wt_GSNO -2.92402824575823 12.8707284018497 1.35908019280542e-09 4.57145155761824e-09 -TR4669|c0_g2_i1 wt_37 wt_GSNO -10.5373989771184 13.0207784411552 2.87822490296537e-08 8.87452678414323e-08 -TR2672|c0_g1_i1 wt_37 wt_GSNO 2.77705541360002 10.2430402179839 7.41806563943484e-08 2.11129560506992e-07 -TR4163|c0_g1_i1 wt_37 wt_GSNO 0.420123134789911 14.7306522277754 2.74345107938324e-06 7.25054928122714e-06 -TR127|c1_g1_i1 wt_37 wt_GSNO 3.26487561187968 9.85808314705506 6.1191913603037e-06 1.50940053554158e-05 -TR2107|c1_g1_i1 wt_37 wt_GSNO 2.54741701164587 11.489948731934 1.24782096095324e-05 2.88558597220436e-05 -TR2779|c0_g1_i1 wt_37 wt_GSNO -0.571512278204146 14.0677635717422 7.39487278515011e-05 0.000160947231206208 -TR1894|c2_g1_i1 wt_37 wt_GSNO 1.88989717290856 9.93884262525918 0.00064827406279645 0.00133256335130381 -TR5055|c0_g2_i1 wt_37 wt_GSNO 1.89504810994952 10.6064804346292 0.00584438080176016 0.011381162613954 -TR3807|c0_g1_i1 wt_37 wt_GSNO 2.66606066906632 8.56455983886691 0.0188051214716541 0.0347894747225602 -TR5212|c0_g1_i1 wt_37 wt_GSNO -0.867441722907523 13.0312878134755 0.0313380642877521 0.055214684697468 -TR1449|c0_g1_i1 wt_37 wt_GSNO 0.636828244112651 13.716963541734 0.0836258106887223 0.140643408885578 -TR1837|c2_g1_i1 wt_37 wt_GSNO -2.70136949048315 8.19724487849862 0.11443273811818 0.184087448277072 -TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06021338602227 9.44252758756623 0.17021260004507 0.262411091736149 -TR4084|c0_g1_i1 wt_37 wt_GSNO -0.527027354857722 13.3333941866224 0.195100037539558 0.280916147575458 -TR1891|c0_g1_i1 wt_37 wt_GSNO -0.481344817930584 13.5015018099629 0.197400536134106 0.280916147575458 -TR24|c0_g1_i1 wt_37 wt_GSNO 0.590686928315332 12.3882336221811 0.209814398393357 0.287523434835341 -TR2011|c5_g1_i1 wt_37 wt_GSNO -0.668008806764204 9.63014074618193 0.239244885423374 0.316145027166602 -TR939|c0_g1_i1 wt_37 wt_GSNO -0.361607139894815 13.0833886152319 0.340252678428006 0.434115486270215 -TR5075|c0_g1_i1 wt_37 wt_GSNO 0.617585416067661 10.4358029661318 0.377913209145196 0.466092957945741 -TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0311900896664335 17.1368189470585 0.559289231968699 0.657620159615942 -TR3249|c0_g1_i1 wt_37 wt_GSNO -0.894241538356016 8.33957569586088 0.568752570478653 0.657620159615942 -TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0373200220187202 15.4258149088647 0.636489077475997 0.713639268685208 -TR2182|c3_g2_i6 wt_37 wt_GSNO 0.714549920613349 8.45775163335771 0.790296098133788 0.860028106792652 -TR1982|c2_g1_i1 wt_37 wt_GSNO -0.181275971858276 9.49467590956657 0.873422282667325 0.923332127391172 -TR1678|c0_g1_i1 wt_37 wt_GSNO -0.476606391142577 7.93769527756871 1 1 -TR1122|c0_g1_i1 wt_37 wt_GSNO 0.0647357997613641 8.26206759454538 1 1 +TR131|c0_g1_i1 wt_37 wt_GSNO -5.83642810105669 16.0393552039823 0 0 +TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41398153332839 17.4536476715771 1.21637348346174e-303 2.25029094440421e-302 +TR3091|c0_g1_i1 wt_37 wt_GSNO -4.45237397999856 14.0403314476332 9.11341318887913e-90 1.12398762662843e-88 +TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92554296928641 16.3361450450387 3.69873891948914e-76 3.42133350052745e-75 +TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58730581845079 15.8893922467915 5.42826219868508e-69 4.01691402702696e-68 +TR3854|c0_g1_i1 wt_37 wt_GSNO -0.756824867554791 17.5153344325941 9.93801411860139e-30 6.12844203980419e-29 +TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67125620463691 14.56103285356 1.52685095059931e-26 8.07049788173923e-26 +TR3788|c0_g1_i1 wt_37 wt_GSNO -2.92384493547476 12.8707566447513 2.80716974025173e-26 1.29831600486643e-25 +TR3638|c0_g1_i1 wt_37 wt_GSNO 1.50400807132974 15.1071935803349 1.01131038761579e-25 4.15760937130936e-25 +TR2107|c1_g1_i1 wt_37 wt_GSNO 2.54917839024164 11.4899163098162 1.29813298421564e-11 4.80309204159787e-11 +TR2122|c0_g2_i2 wt_37 wt_GSNO -0.904224916354351 13.8984660083514 5.12805835511887e-07 1.72489235581271e-06 +TR2672|c0_g1_i1 wt_37 wt_GSNO 2.7835273976316 10.2430082688313 1.09649323769354e-05 3.26428239781416e-05 +TR2844|c0_g1_i1 wt_37 wt_GSNO -0.705628684062878 14.1849718403614 1.14691003166444e-05 3.26428239781416e-05 +TR127|c1_g1_i1 wt_37 wt_GSNO 3.25921752655672 9.85805490683478 4.65148368806407e-05 0.000122932068898836 +TR5212|c0_g1_i1 wt_37 wt_GSNO -0.868846907645273 13.0312970321941 8.02549473297866e-05 0.000197962203413474 +TR4669|c0_g2_i1 wt_37 wt_GSNO -10.5376618403783 13.0208222595793 0.000100983795793505 0.000233525027772479 +TR4163|c0_g1_i1 wt_37 wt_GSNO 0.419885302419972 14.7306501662725 0.000212062001530818 0.000461546709214134 +TR5055|c0_g2_i1 wt_37 wt_GSNO 1.89467947607274 10.6064557750525 0.000354706720299247 0.000729119369504007 +TR1894|c2_g1_i1 wt_37 wt_GSNO 1.89765713767963 9.93882107563394 0.00173125775949168 0.00337139668953643 +TR1449|c0_g1_i1 wt_37 wt_GSNO 0.634078352010786 13.7169577495829 0.00217137808425439 0.00401704945587062 +TR2779|c0_g1_i1 wt_37 wt_GSNO -0.57033686484928 14.0677674303448 0.0111989371149329 0.0197314606310723 +TR1891|c0_g1_i1 wt_37 wt_GSNO -0.481534755723158 13.501506224993 0.0143918226007056 0.0242044289193685 +TR3807|c0_g1_i1 wt_37 wt_GSNO 2.66618717222413 8.56454952883374 0.0190046641424073 0.0305727205769162 +TR24|c0_g1_i1 wt_37 wt_GSNO 0.595098414993735 12.3882263577198 0.0313658793311069 0.0483557306354564 +TR939|c0_g1_i1 wt_37 wt_GSNO -0.361675208475799 13.0833927791152 0.0549150321214498 0.0812742475397457 +TR4084|c0_g1_i1 wt_37 wt_GSNO -0.528091154047526 13.333398560375 0.0670751762392915 0.0954531354174533 +TR1837|c2_g1_i1 wt_37 wt_GSNO -2.70993930289112 8.19725290476621 0.0887918514630023 0.121677722375225 +TR5075|c0_g1_i1 wt_37 wt_GSNO 0.614944173796075 10.4357920601168 0.162306513000849 0.214476463608265 +TR4859|c0_g1_i1 wt_37 wt_GSNO 1.05953644928152 9.44251782921817 0.174748084396246 0.222954452505555 +TR2011|c5_g1_i1 wt_37 wt_GSNO -0.669059646383004 9.63015201113972 0.264703411652408 0.32646754103797 +TR1492|c0_g1_i2 wt_37 wt_GSNO 0.031711320644402 17.1368189355291 0.451877741421955 0.539337949439108 +TR3249|c0_g1_i1 wt_37 wt_GSNO -0.891916586965799 8.33958255206055 0.564868681268914 0.653129412717181 +TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0377499361453361 15.4258150009092 0.736032464572516 0.825248520884336 +TR2182|c3_g2_i6 wt_37 wt_GSNO 0.715543556453753 8.45775004801063 0.789411909605702 0.859065901629735 +TR1982|c2_g1_i1 wt_37 wt_GSNO -0.179857779984199 9.4946775424438 0.881459062505158 0.931828151791167 +TR1678|c0_g1_i1 wt_37 wt_GSNO -0.501309819317686 7.93769570375269 1 1 +TR1122|c0_g1_i1 wt_37 wt_GSNO 0.0611166350434577 8.2620697940663 1 1 |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Tue Apr 11 19:55:15 2023 +0000 |
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| @@ -1,38 +1,38 @@ sampleA sampleB logFC logCPM PValue FDR -TR131|c0_g1_i1 wt_37 wt_GSNO -5.82360148900389 16.1142242655408 6.54502972918692e-10 2.42166099979916e-08 -TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41183386172098 17.3836256000268 1.7102544921365e-09 3.16397081045253e-08 -TR3091|c0_g1_i1 wt_37 wt_GSNO -4.43700179801176 14.1203688767724 4.42033048679943e-08 5.45174093371929e-07 -TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58598083708684 15.9280757073272 7.01720228399608e-08 6.49091211269637e-07 -TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92043321768346 16.2716301848411 5.72725934421127e-07 4.23817191471634e-06 -TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67738254434993 14.6016057367881 1.03919750932427e-06 5.8615543150164e-06 -TR3638|c0_g1_i1 wt_37 wt_GSNO 1.50288215872986 15.0600281889274 1.12469315856867e-06 5.8615543150164e-06 -TR3788|c0_g1_i1 wt_37 wt_GSNO -2.93907650045598 12.9393872783943 2.35975448958169e-06 9.70121290161359e-06 -TR3854|c0_g1_i1 wt_37 wt_GSNO -0.759397690410038 17.5353083640786 1.26736309513868e-06 5.8615543150164e-06 -TR2107|c1_g1_i1 wt_37 wt_GSNO 2.46233758474327 11.260249244859 0.000163907571391062 0.000551325467406299 -TR2122|c0_g2_i2 wt_37 wt_GSNO -0.898543060702643 13.9151768182402 0.000124408949544541 0.000460313113314803 -TR2844|c0_g1_i1 wt_37 wt_GSNO -0.712202725875737 14.1973066750225 0.000243984033514546 0.000752284103336518 -TR5212|c0_g1_i1 wt_37 wt_GSNO -0.87701850957337 13.0391017777502 0.000473838954429694 0.00134861856260759 -TR4163|c0_g1_i1 wt_37 wt_GSNO 0.417694804483349 14.7107025605232 0.000805848497363634 0.00212974245731817 -TR2672|c0_g1_i1 wt_37 wt_GSNO 2.90562993555483 9.81450205355949 0.00822748279906008 0.0169120479758457 -TR1449|c0_g1_i1 wt_37 wt_GSNO 0.640011354440497 13.6755402195434 0.00227354555819909 0.00560807904355776 -TR127|c1_g1_i1 wt_37 wt_GSNO 3.09466453837236 9.33233275488244 0.00997545255499303 0.0184545872267371 -TR1894|c2_g1_i1 wt_37 wt_GSNO 1.8273232048322 9.47625819175118 0.0170307015491222 0.0286425435144327 -TR5055|c0_g2_i1 wt_37 wt_GSNO 1.79897959483123 10.2910629958573 0.0144290410083875 0.025422596062397 -TR939|c0_g1_i1 wt_37 wt_GSNO -0.363394684962815 13.0708604932728 0.00579686595094712 0.0134052525115652 -TR1837|c2_g1_i1 wt_37 wt_GSNO -2.21418127698954 7.02378849272624 0.0306005987832276 0.0471759231241425 -TR1891|c0_g1_i1 wt_37 wt_GSNO -0.477062796219233 13.500309435849 0.00675073796972544 0.0146927826399907 -TR3807|c0_g1_i1 wt_37 wt_GSNO 1.91879773659378 7.35599058475032 0.0402625583382777 0.0572967176352414 -TR2779|c0_g1_i1 wt_37 wt_GSNO -0.600036558858359 14.0748557225205 0.00991998269314111 0.0184545872267371 -TR24|c0_g1_i1 wt_37 wt_GSNO 0.588796779058576 12.310400953631 0.0185008090691583 0.0297621711112546 -TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06036244689068 8.9138577436531 0.104550838513832 0.143273371296733 -TR4084|c0_g1_i1 wt_37 wt_GSNO -0.567278869966665 13.330468891507 0.0372234219214301 0.0550906644437166 -TR2011|c5_g1_i1 wt_37 wt_GSNO -0.789577978066661 9.33004998835934 0.161975973261362 0.206659000367944 +TR131|c0_g1_i1 wt_37 wt_GSNO -5.82360148900389 16.1142242655408 6.54502972918681e-10 2.42166099979912e-08 +TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41183386172098 17.3836256000268 1.71025449213644e-09 3.1639708104524e-08 +TR3091|c0_g1_i1 wt_37 wt_GSNO -4.43700179801175 14.1203688767724 4.42033048679932e-08 5.45174093371916e-07 +TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58598083708684 15.9280757073272 7.01720228399587e-08 6.49091211269618e-07 +TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92043321768345 16.2716301848411 5.72725934421077e-07 4.23817191471597e-06 +TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67738254434994 14.6016057367881 1.03919750932434e-06 5.86155431501655e-06 +TR3638|c0_g1_i1 wt_37 wt_GSNO 1.50288215872986 15.0600281889274 1.12469315856861e-06 5.86155431501655e-06 +TR3788|c0_g1_i1 wt_37 wt_GSNO -2.93907650045598 12.9393872783943 2.35975448958161e-06 9.7012129016133e-06 +TR3854|c0_g1_i1 wt_37 wt_GSNO -0.759397690410033 17.5353083640786 1.26736309513871e-06 5.86155431501655e-06 +TR2107|c1_g1_i1 wt_37 wt_GSNO 2.46233758474327 11.260249244859 0.000163907571391064 0.000551325467406306 +TR2122|c0_g2_i2 wt_37 wt_GSNO -0.898543060702644 13.9151768182402 0.000124408949544541 0.000460313113314803 +TR2844|c0_g1_i1 wt_37 wt_GSNO -0.712202725875737 14.1973066750225 0.000243984033514541 0.000752284103336501 +TR5212|c0_g1_i1 wt_37 wt_GSNO -0.877018509573372 13.0391017777502 0.000473838954429683 0.00134861856260756 +TR4163|c0_g1_i1 wt_37 wt_GSNO 0.417694804483346 14.7107025605232 0.000805848497363675 0.00212974245731828 +TR2672|c0_g1_i1 wt_37 wt_GSNO 2.90562993555483 9.81450205355949 0.0082274827990601 0.0169120479758458 +TR1449|c0_g1_i1 wt_37 wt_GSNO 0.640011354440497 13.6755402195434 0.00227354555819906 0.00560807904355767 +TR127|c1_g1_i1 wt_37 wt_GSNO 3.09466453837236 9.33233275488244 0.00997545255499306 0.0184545872267372 +TR1894|c2_g1_i1 wt_37 wt_GSNO 1.82732320483219 9.47625819175118 0.0170307015491221 0.0286425435144326 +TR5055|c0_g2_i1 wt_37 wt_GSNO 1.79897959483123 10.2910629958573 0.0144290410083874 0.0254225960623969 +TR939|c0_g1_i1 wt_37 wt_GSNO -0.363394684962811 13.0708604932728 0.00579686595094751 0.0134052525115661 +TR1837|c2_g1_i1 wt_37 wt_GSNO -2.21418127698954 7.02378849272624 0.0306005987832277 0.0471759231241427 +TR1891|c0_g1_i1 wt_37 wt_GSNO -0.477062796219235 13.500309435849 0.00675073796972539 0.0146927826399906 +TR3807|c0_g1_i1 wt_37 wt_GSNO 1.91879773659378 7.35599058475032 0.0402625583382779 0.0572967176352417 +TR2779|c0_g1_i1 wt_37 wt_GSNO -0.600036558858356 14.0748557225205 0.0099199826931416 0.0184545872267372 +TR24|c0_g1_i1 wt_37 wt_GSNO 0.588796779058576 12.310400953631 0.0185008090691582 0.0297621711112545 +TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06036244689069 8.9138577436531 0.104550838513831 0.143273371296732 +TR4084|c0_g1_i1 wt_37 wt_GSNO -0.567278869966665 13.330468891507 0.03722342192143 0.0550906644437164 +TR2011|c5_g1_i1 wt_37 wt_GSNO -0.78957797806666 9.33004998835934 0.161975973261362 0.206659000367945 TR2182|c3_g2_i6 wt_37 wt_GSNO 1.02218394394404 7.37517597546907 0.329234058043314 0.406055338253421 -TR5075|c0_g1_i1 wt_37 wt_GSNO 0.549449880041588 10.1791103984097 0.127566698813275 0.168570280574684 -TR4669|c0_g2_i1 wt_37 wt_GSNO -6.27345157840298 13.126293325041 0.423017017822531 0.489113426857301 -TR1678|c0_g1_i1 wt_37 wt_GSNO -0.330222398445961 5.95523974949609 0.735881722270124 0.79829094077818 -TR1122|c0_g1_i1 wt_37 wt_GSNO 0.193564460109425 7.01613737702005 0.875819231521416 0.875819231521416 -TR3249|c0_g1_i1 wt_37 wt_GSNO -0.276543877903423 7.32180296800742 0.776715509946338 0.79829094077818 -TR1982|c2_g1_i1 wt_37 wt_GSNO -0.131251756802268 9.08566155151058 0.763275890632561 0.79829094077818 -TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0407242590322052 15.424279874284 0.616230913043451 0.69092556916993 -TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0323916193661019 17.1363857315734 0.39613877470297 0.472810795613223 +TR5075|c0_g1_i1 wt_37 wt_GSNO 0.549449880041589 10.1791103984097 0.127566698813275 0.168570280574685 +TR4669|c0_g2_i1 wt_37 wt_GSNO -6.27345157840299 13.126293325041 0.42301701782253 0.4891134268573 +TR1678|c0_g1_i1 wt_37 wt_GSNO -0.330222398445961 5.95523974949609 0.735881722270124 0.798290940778181 +TR1122|c0_g1_i1 wt_37 wt_GSNO 0.193564460109423 7.01613737702005 0.875819231521417 0.875819231521417 +TR3249|c0_g1_i1 wt_37 wt_GSNO -0.276543877903423 7.32180296800742 0.776715509946338 0.798290940778181 +TR1982|c2_g1_i1 wt_37 wt_GSNO -0.131251756802266 9.08566155151058 0.763275890632564 0.798290940778181 +TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0407242590322026 15.424279874284 0.616230913043476 0.690925569169958 +TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0323916193660987 17.1363857315734 0.39613877470302 0.472810795613282 |
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| b |
| b'@@ -1,39 +1,39 @@\n sampleA\tsampleB\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR4277|c0_g1_i1\twt_37\twt_ph8\t4705.34614971641\t162.902721493704\t2434.12443560506\t4.85332629705957\t0.130960775627329\t37.0593887659196\t1.26787233139066e-300\t4.81791485928452e-299\n-TR131|c0_g1_i1\twt_37\twt_ph8\t32.0461070493257\t1436.30905989883\t734.177583474076\t-5.49708942597102\t0.198466854292743\t-27.6977707212645\t7.42748041559505e-169\t1.41122127896306e-167\n-TR3091|c0_g1_i1\twt_37\twt_ph8\t20.4914097091341\t321.651020117047\t171.071214913091\t-3.98630633515117\t0.247421953542878\t-16.1113687693051\t2.12272588309166e-58\t2.47056970916163e-57\n-TR4761|c0_g1_i1\twt_37\twt_ph8\t2012.6141923276\t384.620292965437\t1198.61724264652\t2.3876556238738\t0.148312557773369\t16.0988095662291\t2.60059969385434e-58\t2.47056970916163e-57\n-TR5075|c0_g1_i1\twt_37\twt_ph8\t19.3833722195684\t136.98672801182\t78.1850501156942\t-2.81556781738656\t0.271397918695418\t-10.3743161735385\t3.24527446090745e-25\t2.46640859028966e-24\n-TR2779|c0_g1_i1\twt_37\twt_ph8\t191.51955185349\t1058.15934185376\t624.839446853626\t-2.46872482043468\t0.248047686960726\t-9.95262181511717\t2.45625242439133e-23\t1.55562653544784e-22\n-TR1891|c0_g1_i1\twt_37\twt_ph8\t131.416087212132\t376.595292171713\t254.005689691923\t-1.51763504949468\t0.1638333296262\t-9.26328637132193\t1.98234808919548e-20\t1.07613181984897e-19\n-TR1492|c0_g1_i2\twt_37\twt_ph8\t2006.11782336441\t890.823502721036\t1448.47066304272\t1.17138763330801\t0.12740597231583\t9.19413440371721\t3.78025797563847e-20\t1.79562253842827e-19\n-TR2487|c0_g1_i1\twt_37\twt_ph8\t418.818667162757\t965.862817209246\t692.340742186001\t-1.2068861494209\t0.138672539999103\t-8.70313725722989\t3.22833072204789e-18\t1.36307297153133e-17\n-TR3638|c0_g1_i1\twt_37\twt_ph8\t713.131183384274\t326.063958913919\t519.597571149096\t1.12959116050602\t0.141514345090045\t7.98216717737888\t1.43786102301427e-15\t5.46387188745423e-15\n-TR2122|c0_g2_i2\twt_37\twt_ph8\t146.135958637131\t360.821667264163\t253.478812950647\t-1.30611123021679\t0.169971549866392\t-7.68429323168187\t1.53843927144304e-14\t5.31460839225778e-14\n-TR2107|c1_g1_i1\twt_37\twt_ph8\t59.5986596731862\t1.89840873462066\t30.7485342039034\t4.94663101068376\t0.648801734442531\t7.62425676148051\t2.45444399373987e-14\t7.77240598017624e-14\n-TR1479|c0_g1_i1\twt_37\twt_ph8\t158.005105094407\t334.827472148091\t246.416288621249\t-1.08064044509537\t0.1658526880096\t-6.5156643408325\t7.23686413447617e-11\t2.11539105469303e-10\n-TR24|c0_g1_i1\twt_37\twt_ph8\t85.6614643869141\t199.923709280262\t142.792586833588\t-1.2309601921531\t0.197065470330035\t-6.24645296860761\t4.19878369504606e-10\t1.13966986008393e-09\n-TR4163|c0_g1_i1\twt_37\twt_ph8\t424.593720981574\t227.471218917767\t326.03246994967\t0.902378343080323\t0.156120482680011\t5.78001251078543\t7.46950706226027e-09\t1.89227512243927e-08\n-TR1449|c0_g1_i1\twt_37\twt_ph8\t220.782434528097\t117.26089394399\t169.021664236043\t0.916182468982544\t0.175267159439457\t5.22734819182726\t1.71958482582468e-07\t4.0840139613336e-07\n-TR2278|c0_g1_i1\twt_37\twt_ph8\t594.657329919233\t348.341653317169\t471.499491618201\t0.77372548280461\t0.158144801146882\t4.8925129197639\t9.95565784679233e-07\t2.22538234222417e-06\n-TR5055|c0_g2_i1\twt_37\twt_ph8\t28.6665933385886\t6.05959103586122\t17.3630921872249\t2.22056293047175\t0.515653625436263\t4.30630722045843\t1.66002467176804e-05\t3.50449652928809e-05\n-TR127|c1_g1_i1\twt_37\twt_ph8\t16.3791628279609\t1.58772512712498\t8.98344397754296\t3.35782864860774\t0.805715621214412\t4.16751091848842\t3.07943766984562e-05\t6.15887533969124e-05\n-TR1894|c2_g1_i1\twt_37\twt_ph8\t16.2826445742552\t1.67571344127509\t8.97917900776516\t3.31835899440704\t0.806156235895963\t4.1162728099709\t3.85048512190331e-05\t7.31592173161629e-05\n-TR2672|c0_g1_i1\twt_37\twt_ph8\t22.3129914439134\t7.89947501226409\t15.1062332280887\t1.4879160019133\t0.490304786216723\t3.03467566244728\t0.00240794483755529\t0.00435723351557623\n-TR4084|c0_g1_i1\twt_37\twt_ph8\t113.2594381118\t173.837287636503\t143.548362874151\t-0.610546095515356\t0.203809508378262\t-2.99567032163292\t0.00273842322103228\t0.00473000374541939\n-TR4859|c0_g1_i1\twt_37\twt_ph8\t8.91205730249659\t1'..b'09\t5.7800125107855\t7.46950706225728e-09\t1.89227512243851e-08\n+TR1449|c0_g1_i1\twt_37\twt_ph8\t220.782434528097\t117.26089394399\t169.021664236043\t0.916182468982546\t0.175267159439456\t5.22734819182728\t1.71958482582447e-07\t4.08401396133312e-07\n+TR2278|c0_g1_i1\twt_37\twt_ph8\t594.657329919233\t348.341653317169\t471.499491618201\t0.773725482804612\t0.158144801146882\t4.8925129197639\t9.95565784679224e-07\t2.22538234222415e-06\n+TR5055|c0_g2_i1\twt_37\twt_ph8\t28.6665933385886\t6.05959103586122\t17.3630921872249\t2.22056293047174\t0.515653625436262\t4.30630722045843\t1.66002467176799e-05\t3.50449652928799e-05\n+TR127|c1_g1_i1\twt_37\twt_ph8\t16.3791628279609\t1.58772512712498\t8.98344397754296\t3.35782864860774\t0.805715621214412\t4.16751091848842\t3.0794376698456e-05\t6.15887533969119e-05\n+TR1894|c2_g1_i1\twt_37\twt_ph8\t16.2826445742552\t1.67571344127509\t8.97917900776516\t3.31835899440704\t0.806156235895962\t4.1162728099709\t3.85048512190321e-05\t7.31592173161609e-05\n+TR2672|c0_g1_i1\twt_37\twt_ph8\t22.3129914439134\t7.89947501226409\t15.1062332280887\t1.4879160019133\t0.490304786216721\t3.03467566244728\t0.00240794483755522\t0.00435723351557611\n+TR4084|c0_g1_i1\twt_37\twt_ph8\t113.2594381118\t173.837287636503\t143.548362874151\t-0.610546095515353\t0.203809508378262\t-2.99567032163291\t0.0027384232210324\t0.0047300037454196\n+TR4859|c0_g1_i1\twt_37\twt_ph8\t8.91205730249659\t1.28188505334354\t5.09697117792006\t2.79846628921536\t0.94330374949058\t2.96666507551426\t0.00301048704228199\t0.00497384815681373\n+TR1678|c0_g1_i1\twt_37\twt_ph8\t0.738899982352077\t7.85275634721875\t4.29582816478541\t-3.47431884008145\t1.21198503063676\t-2.8666351087324\t0.00414861034620891\t0.00656863304816411\n+TR3807|c0_g1_i1\twt_37\twt_ph8\t4.23896204531587\t0.352255997713617\t2.29560902151474\t3.60257127355045\t1.494771199452\t2.41011552461755\t0.0159474699414716\t0.0242401543110368\n+TR1859|c3_g1_i1\twt_37\twt_ph8\t0.361569353912422\t2.25550826604853\t1.30853880998047\t-2.58650633406891\t1.68391965639604\t-1.53600340980911\t0.124537544060973\t0.181135380859874\n+TR3249|c0_g1_i1\twt_37\twt_ph8\t1.36481976577862\t4.37661229401476\t2.87071602989669\t-1.67837058189371\t1.10474169040967\t-1.51924254915312\t0.128701454821489\t0.181135380859874\n+TR2090|c0_g1_i1\twt_37\twt_ph8\t0\t5.87877087384675\t2.93938543692337\t-4.93100736412615\t3.57047444665656\t-1.38105101655149\t0.167263275059569\t0.227000159009415\n+TR1982|c2_g1_i1\twt_37\twt_ph8\t7.00144976454503\t11.520013112092\t9.26073143831853\t-0.727260398375605\t0.567300823658433\t-1.28196605406919\t0.199854554547713\t0.261878381821141\n+TR1837|c2_g1_i1\twt_37\twt_ph8\t0.377330628439655\t1.67813520813222\t1.02773291828594\t-2.14007669057536\t1.85335822648042\t-1.15470212935544\t0.248212427250958\t0.314402407851213\n+TR5212|c0_g1_i1\twt_37\twt_ph8\t80.2050001877881\t94.8352723753388\t87.5201362815635\t-0.236625075567937\t0.216144030335029\t-1.09475646956875\t0.273623341840839\t0.335409257740383\n+TR3854|c0_g1_i1\twt_37\twt_ph8\t1925.26464813324\t2107.16376011081\t2016.21420412203\t-0.130625245556186\t0.130881633584188\t-0.998041069468797\t0.318259444082749\t0.377933089848265\n+TR2844|c0_g1_i1\twt_37\twt_ph8\t193.030766468894\t213.82243412349\t203.426600296192\t-0.144061748535941\t0.171730922251619\t-0.838880654963595\t0.401536284440309\t0.450271927171227\n+TR1122|c0_g1_i1\twt_37\twt_ph8\t1.69354093201913\t0.660517838352177\t1.17702938518565\t1.39462173786331\t1.66721495733336\t0.83649785633758\t0.402874882205835\t0.450271927171227\n+TR2011|c5_g1_i1\twt_37\twt_ph8\t6.84875389533898\t4.81927837273561\t5.8340161340373\t0.483956961494249\t0.73923753588747\t0.654670438120068\t0.512679962329314\t0.556623959100398\n+TR2182|c3_g2_i6\twt_37\twt_ph8\t2.76248771922916\t1.94482465855284\t2.353656188891\t0.516404389322082\t1.10366040723296\t0.467901526536394\t0.639855011782969\t0.675402512437579\n+TR3788|c0_g1_i1\twt_37\twt_ph8\t23.7579432209456\t26.0024682525169\t24.8802057367313\t-0.125340757750782\t0.352879389384873\t-0.35519432849074\t0.72244401329073\t0.741969527163452\n+TR939|c0_g1_i1\twt_37\twt_ph8\t103.002135647151\t102.820214322362\t102.911174984756\t0.000973457550311695\t0.195891269167832\t0.00496937691223835\t0.996035027203895\t0.996035027203895\n' |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf |
| b |
| Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Tue Apr 11 19:55:15 2023 +0000 |
| b |
| @@ -1,39 +1,39 @@ sampleA sampleB logFC logCPM PValue FDR -TR131|c0_g1_i1 wt_37 wt_ph8 -5.83867709149149 16.0447742820606 3.67956255674e-64 1.3982337715612e-62 -TR3091|c0_g1_i1 wt_37 wt_ph8 -4.35104356420213 13.9337836495047 7.47918124727105e-59 1.4210444369815e-57 -TR4277|c0_g1_i1 wt_37 wt_ph8 4.51249642920563 17.4585638169146 1.30305812944242e-53 1.65054029729373e-52 -TR5075|c0_g1_i1 wt_37 wt_ph8 -3.18286810352713 12.8084040893566 8.25600206225396e-24 7.84320195914126e-23 -TR2107|c1_g1_i1 wt_37 wt_ph8 4.48477961203985 11.2510359028096 1.80754966502889e-22 1.37373774542196e-21 -TR2779|c0_g1_i1 wt_37 wt_ph8 -2.75442228103487 15.7797198210508 8.23352696880425e-15 5.21456708024269e-14 -TR1891|c0_g1_i1 wt_37 wt_ph8 -1.85607282303223 14.4424161372431 4.82341414399837e-12 2.61842482102769e-11 -TR4761|c0_g1_i1 wt_37 wt_ph8 2.05815692521639 16.4916266891202 6.53530817860542e-12 3.10427138483757e-11 -TR1479|c0_g1_i1 wt_37 wt_ph8 -1.43256512308186 14.3771181295432 1.13197856555697e-09 4.77946505457389e-09 -TR2122|c0_g2_i2 wt_37 wt_ph8 -1.63807722824331 14.4300672231344 2.54380104198531e-09 9.66644395954419e-09 -TR24|c0_g1_i1 wt_37 wt_ph8 -1.56169455062581 13.613754007054 1.01137959952142e-08 3.49385679834671e-08 -TR2487|c0_g1_i1 wt_37 wt_ph8 -1.52157644373511 15.8810635663776 2.37540305111961e-07 7.52210966187877e-07 -TR4084|c0_g1_i1 wt_37 wt_ph8 -0.991060679215133 13.5661427311877 4.21767858359174e-07 1.23285989366528e-06 -TR1678|c0_g1_i1 wt_37 wt_ph8 -3.62458577193226 9.02581543875671 1.43837087677047e-05 3.90414952266271e-05 -TR127|c1_g1_i1 wt_37 wt_ph8 2.90111481011278 9.73961125813442 2.21824302925283e-05 5.61954900744051e-05 -TR1894|c2_g1_i1 wt_37 wt_ph8 2.85359093751189 9.70265145133598 3.82707393478771e-05 9.08930059512081e-05 -TR5055|c0_g2_i1 wt_37 wt_ph8 1.8545312748531 10.5508309427169 0.000561739096452478 0.0012556520979526 -TR2090|c0_g1_i1 wt_37 wt_ph8 -5.85461418677349 8.72713197001274 0.000625444406369261 0.00132038263566844 -TR4859|c0_g1_i1 wt_37 wt_ph8 2.31469487039419 9.12085022188999 0.00236706272759891 0.00473412545519782 -TR1492|c0_g1_i2 wt_37 wt_ph8 0.847097868783511 16.8160271449712 0.00265383515294934 0.00504228679060374 -TR3638|c0_g1_i1 wt_37 wt_ph8 0.812580107843708 15.3469752226999 0.00403607816905259 0.00730337954399992 -TR3807|c0_g1_i1 wt_37 wt_ph8 2.92018331334326 8.37863764275674 0.0119536481076316 0.0206472103677272 -TR1449|c0_g1_i1 wt_37 wt_ph8 0.576747771663695 13.7363876885022 0.0130185393324759 0.0215088910710471 -TR1982|c2_g1_i1 wt_37 wt_ph8 -1.11743546508384 9.86122459596308 0.024471659211255 0.0382656346855499 -TR2672|c0_g1_i1 wt_37 wt_ph8 1.09825528852042 10.4080374441724 0.025174759661546 0.0382656346855499 -TR3249|c0_g1_i1 wt_37 wt_ph8 -2.00776956676821 8.66772655901099 0.0275363688345113 0.0402454621427472 -TR5212|c0_g1_i1 wt_37 wt_ph8 -0.582012857882519 12.8600915149255 0.0318599127004672 0.0448398771339909 -TR4163|c0_g1_i1 wt_37 wt_ph8 0.585935901552979 14.6858409740027 0.0333717283041774 0.0452902026985264 -TR2844|c0_g1_i1 wt_37 wt_ph8 -0.484938504762758 14.0537413817093 0.0410237194953782 0.0537552186491163 -TR1859|c3_g1_i1 wt_37 wt_ph8 -2.64648031785777 8.0811923384908 0.0677782555815868 0.0858524570700099 -TR2278|c0_g1_i1 wt_37 wt_ph8 0.462893051132405 15.2205527935145 0.0990317248813937 0.121393727273966 -TR3854|c0_g1_i1 wt_37 wt_ph8 -0.45233145936844 17.3656486469949 0.115995274036176 0.13774438791796 -TR3788|c0_g1_i1 wt_37 wt_ph8 -0.512277745155381 11.1125640718165 0.129462204245195 0.149077689736891 -TR939|c0_g1_i1 wt_37 wt_ph8 -0.343195417039388 13.0829763503018 0.196684960972624 0.219824368145874 -TR1837|c2_g1_i1 wt_37 wt_ph8 -2.21076601464763 7.9226544260522 0.248563909756302 0.269869387735413 -TR1122|c0_g1_i1 wt_37 wt_ph8 0.860567840252952 7.98418712954456 0.72405804618472 0.764283493194982 -TR2011|c5_g1_i1 wt_37 wt_ph8 0.075980865610854 9.27931055760989 0.901508002533997 0.925873083683564 -TR2182|c3_g2_i6 wt_37 wt_ph8 0.147124070779728 8.45393312498213 1 1 +TR131|c0_g1_i1 wt_37 wt_ph8 -5.84041934032622 16.0447738584896 2.64843647765193e-68 1.00640586150773e-66 +TR4277|c0_g1_i1 wt_37 wt_ph8 4.51251378503982 17.458563860849 7.87456958793119e-51 1.49616822170693e-49 +TR3091|c0_g1_i1 wt_37 wt_ph8 -4.33866462808288 13.9337820695818 2.36438873567113e-40 2.99489239851676e-39 +TR5075|c0_g1_i1 wt_37 wt_ph8 -3.18184004176717 12.8084012906916 4.32969562983877e-23 4.11321084834683e-22 +TR2779|c0_g1_i1 wt_37 wt_ph8 -2.76000097034818 15.7797193517192 7.02929665566158e-23 5.3422654583028e-22 +TR2107|c1_g1_i1 wt_37 wt_ph8 4.48695752844007 11.251039090086 2.85694633276303e-20 1.80939934408325e-19 +TR4761|c0_g1_i1 wt_37 wt_ph8 2.0579616780365 16.4916266757798 1.87157355154512e-14 1.01599707083878e-13 +TR1891|c0_g1_i1 wt_37 wt_ph8 -1.85558303182422 14.4424152648443 1.3549609315801e-11 6.43606442500547e-11 +TR2122|c0_g2_i2 wt_37 wt_ph8 -1.63829756449903 14.4300663727902 1.82580551883595e-09 7.70895663508514e-09 +TR2487|c0_g1_i1 wt_37 wt_ph8 -1.52256386898699 15.8810632159828 1.00076368146348e-08 3.80290198956123e-08 +TR24|c0_g1_i1 wt_37 wt_ph8 -1.56069263322937 13.6137525216945 2.0641918619938e-08 7.13084461416041e-08 +TR1479|c0_g1_i1 wt_37 wt_ph8 -1.43017641947686 14.3771173732228 1.25129096758536e-07 3.96242139735364e-07 +TR127|c1_g1_i1 wt_37 wt_ph8 2.89378247411933 9.73961391632741 1.77483025831263e-06 5.18796537045229e-06 +TR1894|c2_g1_i1 wt_37 wt_ph8 2.84455594181396 9.70265363738305 3.80774768997069e-06 1.03353151584919e-05 +TR2090|c0_g1_i1 wt_37 wt_ph8 -5.84865009980137 8.72712853989006 7.1017296397318e-06 1.79910484206539e-05 +TR5055|c0_g2_i1 wt_37 wt_ph8 1.82971910256975 10.5508300754678 1.05374662314498e-05 2.50264822996933e-05 +TR1678|c0_g1_i1 wt_37 wt_ph8 -3.62297933758159 9.02581162405914 1.85386281004691e-05 4.1439286342225e-05 +TR4084|c0_g1_i1 wt_37 wt_ph8 -0.989047817791601 13.5661419902701 0.000266385708775898 0.000562369829638008 +TR1492|c0_g1_i2 wt_37 wt_ph8 0.846946606328173 16.816027085378 0.00111844437365923 0.00223688874731846 +TR4859|c0_g1_i1 wt_37 wt_ph8 2.31297110196869 9.12085217163192 0.00169405620519211 0.00321870678986502 +TR3638|c0_g1_i1 wt_37 wt_ph8 0.812150684296427 15.3469750288171 0.00195862604708162 0.0035441804661477 +TR3807|c0_g1_i1 wt_37 wt_ph8 2.91885642490418 8.37863917696072 0.00889981242694952 0.0153724032829128 +TR2672|c0_g1_i1 wt_37 wt_ph8 1.09015105073495 10.4080380170218 0.0113968048117331 0.0188295036019939 +TR3249|c0_g1_i1 wt_37 wt_ph8 -2.00248923602224 8.66772464596919 0.012175839230813 0.0192784121154539 +TR1982|c2_g1_i1 wt_37 wt_ph8 -1.11692146946545 9.86122186982139 0.0254732500230551 0.0380540735981811 +TR4163|c0_g1_i1 wt_37 wt_ph8 0.585493536631111 14.6858406628863 0.0260369977250713 0.0380540735981811 +TR1449|c0_g1_i1 wt_37 wt_ph8 0.579397661518319 13.7363873307119 0.0302958377959148 0.0426385865275838 +TR5212|c0_g1_i1 wt_37 wt_ph8 -0.580254103150409 12.8600901680646 0.0404390149604427 0.054881520303458 +TR1859|c3_g1_i1 wt_37 wt_ph8 -2.66753302288967 8.08119047667972 0.0460728591095077 0.0603713326262514 +TR2844|c0_g1_i1 wt_37 wt_ph8 -0.482774572490911 14.0537407448782 0.0727694305006538 0.0921746119674948 +TR2278|c0_g1_i1 wt_37 wt_ph8 0.462415658712107 15.2205525577595 0.0767838146787893 0.0941220954127095 +TR3854|c0_g1_i1 wt_37 wt_ph8 -0.452545415035422 17.3656485551494 0.080313088818483 0.0953717929719486 +TR3788|c0_g1_i1 wt_37 wt_ph8 -0.50904223856954 11.112562271961 0.177982574706024 0.204949631479664 +TR1837|c2_g1_i1 wt_37 wt_ph8 -2.21377059210539 7.92265348832559 0.23010293924542 0.251432947894972 +TR939|c0_g1_i1 wt_37 wt_ph8 -0.340377492720978 13.0829751506545 0.231582978324316 0.251432947894972 +TR1122|c0_g1_i1 wt_37 wt_ph8 0.90037398238529 7.98418851125693 0.694931998823269 0.733539332091228 +TR2182|c3_g2_i6 wt_37 wt_ph8 0.125015386728524 8.45393207220823 0.999999999999999 1 +TR2011|c5_g1_i1 wt_37 wt_ph8 0.0588147623425484 9.27930953984144 1 1 |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Tue Apr 11 19:55:15 2023 +0000 |
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| @@ -1,39 +1,39 @@ sampleA sampleB logFC logCPM PValue FDR -TR131|c0_g1_i1 wt_37 wt_ph8 -5.89108692370307 16.0946870940125 5.83734002581789e-38 2.2181892098108e-36 -TR4277|c0_g1_i1 wt_37 wt_ph8 4.47812345668175 17.3786096664403 2.84916418820701e-34 5.41341195759331e-33 -TR3091|c0_g1_i1 wt_37 wt_ph8 -4.37454375877296 13.9751350003907 3.03684158911717e-24 3.84666601288175e-23 -TR2779|c0_g1_i1 wt_37 wt_ph8 -2.89398117484377 15.8061264352363 2.71183962208552e-19 2.57624764098124e-18 -TR5075|c0_g1_i1 wt_37 wt_ph8 -3.21512246000432 12.8334153580766 2.25968184332879e-15 1.71735820092988e-14 -TR2107|c1_g1_i1 wt_37 wt_ph8 4.32040270723487 11.0762608486921 1.80270537224079e-11 1.14171340241917e-10 -TR4761|c0_g1_i1 wt_37 wt_ph8 2.00464775189483 16.4172477083723 4.47039820077749e-11 2.42678759470778e-10 -TR1891|c0_g1_i1 wt_37 wt_ph8 -1.89490003648365 14.4620196202787 2.60196088184267e-10 1.23593141887527e-09 -TR2122|c0_g2_i2 wt_37 wt_ph8 -1.68823123696301 14.4430864744705 9.44150971333403e-09 3.98641521229659e-08 -TR24|c0_g1_i1 wt_37 wt_ph8 -1.665273448047 13.6146325155501 3.81691570216026e-08 1.4504279668209e-07 -TR2487|c0_g1_i1 wt_37 wt_ph8 -1.57111929409713 15.8914511338271 9.80135417366341e-08 3.3859223509019e-07 -TR1479|c0_g1_i1 wt_37 wt_ph8 -1.45195340320994 14.3929474544484 4.87972014978913e-07 1.54524471409989e-06 -TR1678|c0_g1_i1 wt_37 wt_ph8 -3.32711159096413 8.62991286220581 2.09660385386406e-05 6.12853434206418e-05 -TR127|c1_g1_i1 wt_37 wt_ph8 2.68488776770857 9.36026180000128 7.01712501052362e-05 0.000190464821714212 -TR1894|c2_g1_i1 wt_37 wt_ph8 2.65840371977461 9.30640094015976 8.26981533784737e-05 0.0002095019885588 -TR2090|c0_g1_i1 wt_37 wt_ph8 -3.12073361486577 8.21515298661506 0.000232532921389064 0.000552265688299028 -TR5055|c0_g2_i1 wt_37 wt_ph8 1.75449782198233 10.3047459168783 0.000592147419555538 0.00125008899683947 -TR4084|c0_g1_i1 wt_37 wt_ph8 -0.990738086664283 13.5812840323914 0.000555059638311732 0.00124072154446152 -TR4859|c0_g1_i1 wt_37 wt_ph8 2.03844841522755 8.5557148387818 0.00395651243262557 0.00791302486525114 -TR3807|c0_g1_i1 wt_37 wt_ph8 2.27805436961797 7.32408068149202 0.00589866928719914 0.0106737825196937 -TR1492|c0_g1_i2 wt_37 wt_ph8 0.80292474159496 16.7717103141256 0.00563666782754467 0.0106737825196937 -TR1859|c3_g1_i1 wt_37 wt_ph8 -2.08358066039446 6.92308482511994 0.0165122223690091 0.0272810630444498 -TR3638|c0_g1_i1 wt_37 wt_ph8 0.765536214533451 15.2959378061905 0.00664915219564581 0.0114848992470246 -TR2672|c0_g1_i1 wt_37 wt_ph8 1.15555384827173 10.1973122527932 0.0181178874953213 0.0286866552009254 -TR3249|c0_g1_i1 wt_37 wt_ph8 -1.48866796495104 8.06119288435276 0.0485882100928285 0.065758173656721 -TR1982|c2_g1_i1 wt_37 wt_ph8 -1.06368641289493 9.64628067316551 0.0416733207176468 0.0609071610488684 +TR131|c0_g1_i1 wt_37 wt_ph8 -5.89108692370307 16.0946870940125 5.83734002581822e-38 2.21818920981092e-36 +TR4277|c0_g1_i1 wt_37 wt_ph8 4.47812345668175 17.3786096664403 2.84916418820709e-34 5.41341195759347e-33 +TR3091|c0_g1_i1 wt_37 wt_ph8 -4.37454375877296 13.9751350003907 3.03684158911758e-24 3.84666601288227e-23 +TR2779|c0_g1_i1 wt_37 wt_ph8 -2.89398117484377 15.8061264352363 2.71183962208562e-19 2.57624764098134e-18 +TR5075|c0_g1_i1 wt_37 wt_ph8 -3.21512246000432 12.8334153580766 2.25968184332891e-15 1.71735820092997e-14 +TR2107|c1_g1_i1 wt_37 wt_ph8 4.32040270723487 11.0762608486921 1.80270537224084e-11 1.1417134024192e-10 +TR4761|c0_g1_i1 wt_37 wt_ph8 2.00464775189483 16.4172477083723 4.47039820077757e-11 2.42678759470782e-10 +TR1891|c0_g1_i1 wt_37 wt_ph8 -1.89490003648365 14.4620196202787 2.6019608818427e-10 1.23593141887528e-09 +TR2122|c0_g2_i2 wt_37 wt_ph8 -1.68823123696301 14.4430864744705 9.44150971333414e-09 3.98641521229664e-08 +TR24|c0_g1_i1 wt_37 wt_ph8 -1.665273448047 13.6146325155501 3.81691570216034e-08 1.45042796682093e-07 +TR2487|c0_g1_i1 wt_37 wt_ph8 -1.57111929409714 15.8914511338271 9.80135417366337e-08 3.38592235090189e-07 +TR1479|c0_g1_i1 wt_37 wt_ph8 -1.45195340320994 14.3929474544484 4.87972014978926e-07 1.54524471409993e-06 +TR1678|c0_g1_i1 wt_37 wt_ph8 -3.32711159096413 8.62991286220581 2.09660385386408e-05 6.12853434206423e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 2.68488776770857 9.36026180000128 7.01712501052367e-05 0.000190464821714214 +TR1894|c2_g1_i1 wt_37 wt_ph8 2.65840371977461 9.30640094015976 8.26981533784744e-05 0.000209501988558802 +TR2090|c0_g1_i1 wt_37 wt_ph8 -3.12073361486577 8.21515298661506 0.000232532921389067 0.000552265688299035 +TR5055|c0_g2_i1 wt_37 wt_ph8 1.75449782198233 10.3047459168783 0.000592147419555542 0.00125008899683948 +TR4084|c0_g1_i1 wt_37 wt_ph8 -0.990738086664284 13.5812840323914 0.000555059638311732 0.00124072154446152 +TR4859|c0_g1_i1 wt_37 wt_ph8 2.03844841522755 8.5557148387818 0.00395651243262561 0.00791302486525122 +TR3807|c0_g1_i1 wt_37 wt_ph8 2.27805436961797 7.32408068149202 0.00589866928719915 0.0106737825196937 +TR1492|c0_g1_i2 wt_37 wt_ph8 0.802924741594956 16.7717103141256 0.00563666782754487 0.0106737825196937 +TR1859|c3_g1_i1 wt_37 wt_ph8 -2.08358066039446 6.92308482511994 0.016512222369009 0.0272810630444497 +TR3638|c0_g1_i1 wt_37 wt_ph8 0.765536214533451 15.2959378061905 0.00664915219564584 0.0114848992470246 +TR2672|c0_g1_i1 wt_37 wt_ph8 1.15555384827173 10.1973122527932 0.0181178874953214 0.0286866552009255 +TR3249|c0_g1_i1 wt_37 wt_ph8 -1.48866796495104 8.06119288435276 0.0485882100928286 0.0657581736567205 +TR1982|c2_g1_i1 wt_37 wt_ph8 -1.06368641289493 9.64628067316551 0.0416733207176469 0.0609071610488685 TR1837|c2_g1_i1 wt_37 wt_ph8 -1.43890969571076 6.48444225997254 0.11393330230991 0.135295796493019 -TR5212|c0_g1_i1 wt_37 wt_ph8 -0.63168831011067 12.8380836623566 0.0369371606978983 0.0561444842608054 -TR4163|c0_g1_i1 wt_37 wt_ph8 0.545743678134199 14.6411189904126 0.0480591953597162 0.065758173656721 -TR1449|c0_g1_i1 wt_37 wt_ph8 0.549932747054717 13.6939664483469 0.0501838693696029 0.065758173656721 -TR2844|c0_g1_i1 wt_37 wt_ph8 -0.508967050135572 14.0451022220879 0.0631262591502691 0.0799599282570075 -TR3854|c0_g1_i1 wt_37 wt_ph8 -0.504473372285636 17.3527799714624 0.0818779321593283 0.100366497485628 -TR1122|c0_g1_i1 wt_37 wt_ph8 0.501746583160273 6.50836597017328 0.579206371120405 0.611384502849316 +TR5212|c0_g1_i1 wt_37 wt_ph8 -0.63168831011067 12.8380836623566 0.0369371606978984 0.0561444842608055 +TR4163|c0_g1_i1 wt_37 wt_ph8 0.545743678134199 14.6411189904126 0.0480591953597163 0.0657581736567205 +TR1449|c0_g1_i1 wt_37 wt_ph8 0.549932747054718 13.6939664483469 0.0501838693696025 0.0657581736567205 +TR2844|c0_g1_i1 wt_37 wt_ph8 -0.508967050135572 14.0451022220879 0.0631262591502692 0.0799599282570077 +TR3854|c0_g1_i1 wt_37 wt_ph8 -0.504473372285636 17.3527799714624 0.0818779321593284 0.100366497485628 +TR1122|c0_g1_i1 wt_37 wt_ph8 0.501746583160273 6.50836597017328 0.579206371120405 0.611384502849317 TR3788|c0_g1_i1 wt_37 wt_ph8 -0.524753873079964 11.0311382344715 0.196342217213272 0.213171550117267 -TR2278|c0_g1_i1 wt_37 wt_ph8 0.424377145183038 15.1829447141358 0.128541258915261 0.148017207235755 +TR2278|c0_g1_i1 wt_37 wt_ph8 0.424377145183046 15.1829447141358 0.128541258915254 0.148017207235747 TR2182|c3_g2_i6 wt_37 wt_ph8 -0.0429471548350905 7.57134083040984 0.954463369529891 0.954463369529891 TR939|c0_g1_i1 wt_37 wt_ph8 -0.398499350568058 13.0523653134109 0.173205070507278 0.193582137625782 TR2011|c5_g1_i1 wt_37 wt_ph8 -0.0410416962762211 8.85697121679121 0.94542366790428 0.954463369529891 |
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| b'@@ -1,40 +1,40 @@\n sampleA\tsampleB\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR2779|c0_g1_i1\twt_GSNO\twt_ph8\t195.849684476753\t966.924129135581\t581.386906806167\t-2.30255444666643\t0.142496869452374\t-16.1586318037394\t9.87286349195067e-59\t3.65295949202175e-57\n-TR1891|c0_g1_i1\twt_GSNO\twt_ph8\t128.246229498835\t343.028289972482\t235.637259735659\t-1.41742353970608\t0.104322254921725\t-13.5869718380762\t4.7847024102546e-42\t8.85169945897101e-41\n-TR4761|c0_g1_i1\twt_GSNO\twt_ph8\t184.029205648389\t351.782300021135\t267.905752834762\t-0.941259207260894\t0.0933372308442124\t-10.0844989587481\t6.46943903995441e-24\t7.97897481594377e-23\n-TR24|c0_g1_i1\twt_GSNO\twt_ph8\t39.3724575919554\t183.288101009647\t111.330279300801\t-2.22846767043702\t0.242443002218043\t-9.19171784728532\t3.8661704482204e-20\t3.57620766460387e-19\n-TR3638|c0_g1_i1\twt_GSNO\twt_ph8\t174.266398355818\t297.555274221606\t235.910836288712\t-0.761689698593786\t0.0969314803260852\t-7.85802193499368\t3.90246977317854e-15\t2.88782763215212e-14\n-TR2122|c0_g2_i2\twt_GSNO\twt_ph8\t190.673533226329\t328.707071692642\t259.690302459485\t-0.789061688115738\t0.103094089827306\t-7.65380139091878\t1.95123561208803e-14\t1.20326196078762e-13\n-TR4669|c0_g2_i1\twt_GSNO\twt_ph8\t165.630009730314\t0\t82.8150048651569\t9.98638581786287\t2.4059110197361\t4.15077105343582\t3.31357095211564e-05\t0.000175145893183255\n-TR2278|c0_g1_i1\twt_GSNO\twt_ph8\t426.804298570637\t315.99710709695\t371.400702833793\t0.433055347501052\t0.106340324733669\t4.07235306630524\t4.65405596936774e-05\t0.000215250088583258\n-TR4084|c0_g1_i1\twt_GSNO\twt_ph8\t115.544575735664\t157.970364768418\t136.757470252041\t-0.444508945050626\t0.160721197310781\t-2.76571449496544\t0.00567982380522758\t0.0233503867548245\n-TR3788|c0_g1_i1\twt_GSNO\twt_ph8\t128.115824993653\t24.010679388938\t76.0632521912957\t2.41599826196159\t0.930388620648254\t2.59676248004649\t0.00941069736444863\t0.0348195802484599\n-TR5075|c0_g1_i1\twt_GSNO\twt_ph8\t8.81552188359314\t126.23137395943\t67.5234479215117\t-3.83892667969009\t1.51640337447055\t-2.53159993199728\t0.011354345783228\t0.0381918903617669\n-TR1492|c0_g1_i2\twt_GSNO\twt_ph8\t1368.89238848897\t813.514514376559\t1091.20345143276\t0.750717599362045\t0.314762309207928\t2.38503015577424\t0.0170777214032423\t0.0526563076599971\n-TR1678|c0_g1_i1\twt_GSNO\twt_ph8\t0.695005959508731\t7.10082184137838\t3.89791390044355\t-3.29023865439926\t1.5074251817588\t-2.18268786684349\t0.0290588040465388\t0.0827058269016874\n-TR1479|c0_g1_i1\twt_GSNO\twt_ph8\t353.92669362375\t305.546165789569\t329.736429706659\t0.212056310257658\t0.102841330599285\t2.0619755600394\t0.0392100628615421\t0.0987833713777749\n-TR1859|c3_g1_i1\twt_GSNO\twt_ph8\t0\t2.05957798928713\t1.02978899464357\t-3.32897459707672\t1.62131131542189\t-2.05326057087961\t0.0400473127207196\t0.0987833713777749\n-TR2844|c0_g1_i1\twt_GSNO\twt_ph8\t220.566338218013\t194.214843050373\t207.390590634193\t0.186796872895526\t0.101161116569868\t1.84652838194517\t0.0648155222548659\t0.149885895214377\n-TR2107|c1_g1_i1\twt_GSNO\twt_ph8\t7.08292121571621\t1.78415791317121\t4.43353956444371\t1.99039306371489\t1.13345482120555\t1.75604093473959\t0.0790814192380851\t0.172118383047597\n-TR2672|c0_g1_i1\twt_GSNO\twt_ph8\t2.07518941673641\t7.44710458698621\t4.76114700186131\t-1.80710364026684\t1.37881760417113\t-1.31061834052603\t0.189986739707575\t0.390528298287793\n-TR4859|c0_g1_i1\twt_GSNO\twt_ph8\t3.10763825129944\t1.1806627783491\t2.14415051482427\t1.36600125700608\t1.2414304168313\t1.10034460126467\t0.271182006077654\t0.528091274993326\n-TR3091|c0_g1_i1\twt_GSNO\twt_ph8\t312.47018793986\t293.531643106953\t303.000915523406\t0.0884824617062972\t0.0884687505769758\t1.00015498273946\t0.317235511103454\t0.572534846407878\n-TR4163|c0_g1_i1\twt_GSNO\twt_ph8\t221.469120691076\t207.118822998308\t214.293971844692\t0.0967338751775769\t0.0982736079923787\t0.984332183927538\t0.32495221012339\t0.572534846407878\n-TR1894|c2_g1_i1\twt_GSNO\twt_ph8\t2.85762748931802\t1.47338219762144\t2.16550484346973\t0.974874448083219\t1.21963227734233\t0.799318340612911\t0.424105846774723\t0.713268924121126\n-TR3249|c0_g1_i1\twt_GSNO\twt_ph8\t2.06512931203634\t4.15451161800812\t3.1098204650222'..b'16569857\t1.8465283819454\t0.0648155222548327\t0.149885895214301\n+TR2107|c1_g1_i1\twt_GSNO\twt_ph8\t7.08292121571621\t1.78415791317121\t4.43353956444371\t1.99039306371489\t1.13345482120575\t1.75604093473928\t0.0790814192381375\t0.172118383047711\n+TR2672|c0_g1_i1\twt_GSNO\twt_ph8\t2.07518941673641\t7.44710458698621\t4.76114700186131\t-1.80710364026684\t1.3788176041713\t-1.31061834052587\t0.189986739707629\t0.390528298287903\n+TR4859|c0_g1_i1\twt_GSNO\twt_ph8\t3.10763825129944\t1.1806627783491\t2.14415051482427\t1.36600125700608\t1.24143041683139\t1.1003446012646\t0.271182006077686\t0.528091274993389\n+TR3091|c0_g1_i1\twt_GSNO\twt_ph8\t312.47018793986\t293.531643106953\t303.000915523406\t0.0884824617062953\t0.0884687505769775\t1.00015498273942\t0.317235511103473\t0.572534846408031\n+TR4163|c0_g1_i1\twt_GSNO\twt_ph8\t221.469120691076\t207.118822998308\t214.293971844692\t0.0967338751775785\t0.098273607992398\t0.984332183927362\t0.324952210123477\t0.572534846408031\n+TR1894|c2_g1_i1\twt_GSNO\twt_ph8\t2.85762748931802\t1.47338219762144\t2.16550484346973\t0.974874448083218\t1.21963227734242\t0.799318340612854\t0.424105846774756\t0.713268924121181\n+TR3249|c0_g1_i1\twt_GSNO\twt_ph8\t2.06512931203634\t4.15451161800812\t3.10982046502223\t-1.06280923847798\t1.42172379433197\t-0.747549729923012\t0.454731796166159\t0.726065302514524\n+TR5212|c0_g1_i1\twt_GSNO\twt_ph8\t102.736339436612\t86.4452993262187\t94.5908193814151\t0.250307109752951\t0.347207101059796\t0.720915871216134\t0.470961277306718\t0.726065302514524\n+TR1122|c0_g1_i1\twt_GSNO\twt_ph8\t1.29006258579706\t0.5946183773076\t0.942340481552333\t1.01745920560277\t1.75106315862354\t0.581052259932512\t0.561205232532948\t1\n+TR2011|c5_g1_i1\twt_GSNO\twt_ph8\t7.597917075274\t4.42090354598533\t6.00941031062966\t0.776221433822191\t1.38068634268979\t0.562199689981717\t0.573979972628469\t0.849490359490134\n+TR1837|c2_g1_i1\twt_GSNO\twt_ph8\t2.16507864525674\t1.46465683073113\t1.81486773799393\t0.574055870722253\t1.31330872914198\t0.437106567545087\t0.662034064585536\t0.882648546299866\n+TR1982|c2_g1_i1\twt_GSNO\twt_ph8\t5.5352448786851\t10.687042573374\t8.11114372602957\t-0.9487458240786\t2.34310116245464\t-0.404910312572544\t0.685543437736728\t0.882648546299866\n+TR2182|c3_g2_i6\twt_GSNO\twt_ph8\t1.29006258579706\t1.76655578876639\t1.52830918728173\t-0.570835750385155\t1.46441538912588\t-0.389804528567465\t0.69668109483689\t0.882648546299866\n+TR1449|c0_g1_i1\twt_GSNO\twt_ph8\t98.9943307118646\t106.843279101242\t102.918804906553\t-0.106933839690289\t0.276431863357607\t-0.386836156987999\t0.698877507680504\t0.882648546299866\n+TR4277|c0_g1_i1\twt_GSNO\twt_ph8\t153.969096204861\t149.159426886469\t151.564261545665\t0.0465928591855008\t0.127909639606227\t0.364263861026722\t0.715660983486378\t0.882648546299866\n+TR3854|c0_g1_i1\twt_GSNO\twt_ph8\t2260.55060252051\t1927.46472630351\t2094.00766441201\t0.229965172704227\t0.793466242289089\t0.289823511635221\t0.771951259799004\t0.910963182508494\n+TR127|c1_g1_i1\twt_GSNO\twt_ph8\t1.20754470361908\t1.49113571265046\t1.34934020813477\t-0.373671738849602\t1.38864714646406\t-0.269090488394471\t0.787860049737076\t0.910963182508494\n+TR2090|c0_g1_i1\twt_GSNO\twt_ph8\t9.46045896251181\t5.6546754787973\t7.55756722065455\t0.740040477295999\t3.75055668025179\t0.19731483627287\t0.843581169905129\t0.945833432923932\n+TR3807|c0_g1_i1\twt_GSNO\twt_ph8\t0.347502979754365\t0.292870809896544\t0.320186894825454\t0.331202385322155\t1.89086385045428\t0.175159298350637\t0.860954465054859\t1\n+TR131|c0_g1_i1\twt_GSNO\twt_ph8\t1275.67603302799\t1312.2934796972\t1293.9847563626\t-0.0408368749216137\t0.405274721880999\t-0.100763439506115\t0.91973825012661\t0.956831887096637\n+TR5055|c0_g2_i1\twt_GSNO\twt_ph8\t5.17791343714095\t5.60171771495863\t5.38981557604979\t-0.113901914254778\t1.2463123048958\t-0.0913911495596612\t0.927181793948442\t0.956831887096637\n+TR939|c0_g1_i1\twt_GSNO\twt_ph8\t92.2508462008296\t94.0990807885678\t93.1749634946987\t-0.0286723936076184\t0.345661698999674\t-0.0829492931689995\t0.933891858779043\t0.956831887096637\n+TR2487|c0_g1_i1\twt_GSNO\twt_ph8\t875.181494043204\t882.631049341941\t878.906271692572\t-0.0122873741271473\t0.22699904980564\t-0.0541296280212096\t0.956831887096637\t0.956831887096637\n' |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf |
| b |
| Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Tue Apr 11 19:55:15 2023 +0000 |
| b |
| @@ -1,40 +1,40 @@ sampleA sampleB logFC logCPM PValue FDR -TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23948335958727 15.9163308249372 1.20766376889896e-237 4.70988869870595e-236 -TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807859120941235 16.8439348559211 2.37986391219743e-61 4.64073462878498e-60 -TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.35697452203657 14.6311197032228 1.60645028176433e-35 2.08838536629363e-34 -TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.880921757190946 14.8138260614735 1.59143301924913e-24 1.5516471937679e-23 -TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.729785350305026 14.7699678361852 6.52776857951534e-13 5.09165949202196e-12 -TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.289859344737128 17.7786469452325 6.1302236270955e-12 3.98464535761207e-11 -TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.702510801497461 14.6355179638282 5.62335492840333e-11 3.133012031539e-10 -TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.490901034745758 15.2921454021456 1.53296499052609e-09 7.47320432881468e-09 -TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16007337608378 13.5636496776551 8.67157466173412e-09 3.75768235341812e-08 -TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.7524485458028 12.8683202800317 5.50095216588421e-08 2.14537134469484e-07 -TR4669|c0_g2_i1 wt_GSNO wt_ph8 10.4044948993067 13.1110475123695 1.35189372056785e-06 4.79307773655872e-06 -TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47698512550917 13.0240883091698 1.80487840553907e-05 5.86585481800198e-05 -TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.272661827455658 15.1172528121102 0.000483095512098729 0.00144928653629619 -TR1678|c0_g1_i1 wt_GSNO wt_ph8 -3.02812287247775 9.36059212330112 0.0074853976481696 0.0208521791627582 -TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.98032359155541 9.36544178725855 0.0305238827180189 0.0756824353198294 -TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.244755727600329 14.4560017424587 0.0310492042337762 0.0756824353198294 -TR1859|c3_g1_i1 wt_GSNO wt_ph8 -4.12978123132011 8.37588761488442 0.0428877609330621 0.0983895691993777 -TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.148576217250104 14.9963238698071 0.0547318692708507 0.11858571675351 -TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.64029381826409 9.53984158811941 0.100507062957769 0.206303971334369 -TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.156926020788278 14.5006265631178 0.113620071038851 0.22155913852576 -TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.3062724221166 8.73091245897321 0.181160758857669 0.3364414093071 -TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.390578563212142 13.8603174460746 0.270419882900116 0.479380701504752 -TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.866592651710305 10.0958159836705 0.312186869456376 0.515984430920105 -TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.989932992780787 8.78384403630691 0.317528880566218 0.515984430920105 -TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.107189584823599 14.0046148411409 0.347278576725125 0.541754579691195 -TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0467513454249246 16.526653433485 0.376403968202147 0.560230359736405 -TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.00369455926223 9.08504250192555 0.387851787509819 0.560230359736405 -TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.310409394484433 13.3365591825697 0.416163942507532 0.572783249883747 -TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.799376994792807 9.70509536731836 0.425915749913555 0.572783249883747 -TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.59484087321072 8.66193471010726 0.588495494688377 0.76504414309489 -TR2090|c0_g1_i1 wt_GSNO wt_ph8 0.766971023107968 9.89421471118339 0.638322407555079 0.8030507707951 -TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0187996511046741 17.0827735361623 0.697507705031756 0.850087515507453 -TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.908051089281089 8.22928258978683 0.753364106379395 0.890339398448377 -TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.0452741219590205 13.4583026590017 0.919111339143084 1 -TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0309689709592036 13.3146949564453 0.956245904999637 1 -TR5055|c0_g2_i1 wt_GSNO wt_ph8 -0.0548476287872344 9.62768102188797 0.999999999999985 1 -TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.517423422896207 8.5297276065799 1 1 -TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.299043611515333 8.4576897025083 1 1 -TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.266132577378544 7.94319410024963 1 1 +TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23950613357817 15.9163032020312 4.60955581344059e-235 1.79772676724183e-233 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807687320151986 16.8439413499966 1.06317515303199e-90 2.07319154841239e-89 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.74688019557381 12.8681343619696 5.1381781460234e-32 6.67963158983042e-31 +TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16553693339805 13.5635491898429 9.2971773987615e-26 9.06474796379246e-25 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.290142827557204 17.7786481597017 1.25773893145984e-24 9.81036366538678e-24 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47729608121809 13.0242288909359 1.10830409992816e-22 7.20397664953306e-22 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.3583596459138 14.6310791041785 1.59601754746587e-15 8.89209776445273e-15 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.879210949997969 14.8138025433621 1.16981383272981e-13 5.70284243455784e-13 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.729742458144456 14.7699470890569 4.10258938208877e-06 1.77778873223847e-05 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.706925054082112 14.6354932126397 1.54507784026086e-05 6.02580357701737e-05 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 10.4046228735587 13.1113136633968 0.000139728809507287 0.000495402142798563 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 -3.01399259671531 9.36047067579877 0.000442811746352842 0.00143913817564674 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.489116151456685 15.2921561061716 0.00123564582245084 0.00370693746735251 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.97628703812853 9.36554809158219 0.00657205660686984 0.0183078719762803 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.27208346223967 15.1172591193697 0.0367666005878079 0.0955931615283007 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 -4.1298851005078 8.3758408307508 0.0437166707415215 0.106559384932459 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.387761437724876 13.8602939725323 0.0668673830079525 0.153401643371185 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.63593346878775 9.53972870485612 0.0715566666179246 0.155039444338837 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.864358765411198 10.0957379798877 0.108379561457656 0.222463310360452 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.312770273727969 13.3365736924153 0.135331780456409 0.263896971889998 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.241817510473408 14.4560087242059 0.15465951473335 0.287224813076222 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.14889261782812 14.9963282436933 0.186547888961471 0.324612319602237 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.30848594262338 8.73097118348756 0.191438034637217 0.324612319602237 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.790825548309762 9.70516893221035 0.218107108399401 0.354424051149027 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.155999611692108 14.5006318412937 0.284866034395977 0.444391013657724 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.986980002958084 8.78386674332455 0.331299000761855 0.496948501142782 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 -0.985518730250915 9.08501700013798 0.456425031570127 0.65928060115685 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.105816203369183 14.0046181837143 0.523017417566317 0.728488545895941 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0464385825187709 16.5266539544117 0.56789954734259 0.759378620070234 +TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0192051247671651 17.0827736541362 0.598052390607106 0.759378620070234 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.590866113458774 8.6619486530175 0.603608646722493 0.759378620070234 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 0.774122590048598 9.89437120476407 0.740004802646486 0.88514773566839 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.904237754221878 8.22931948652769 0.748971160950176 0.88514773566839 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.0429337811569824 13.4582943043574 0.870095339425673 0.988074012458205 +TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0314734152791246 13.3146965055009 0.886733088103517 0.988074012458205 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 -0.0547681668951162 9.62768076070569 1 1 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.52401851151559 8.52973766897149 1 1 +TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.306284780231878 8.45768988187045 1 1 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.273602957097835 7.94319392916032 1 1 |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf |
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| Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Tue Apr 11 19:55:15 2023 +0000 |
| b |
| b'@@ -1,40 +1,40 @@\n sampleA\tsampleB\tlogFC\tlogCPM\tPValue\tFDR\n-TR2779|c0_g1_i1\twt_GSNO\twt_ph8\t-2.23795519272237\t15.9076254017254\t2.92187316761645e-09\t1.13953053537042e-07\n-TR1492|c0_g1_i2\twt_GSNO\twt_ph8\t0.807554446371668\t16.8426446227048\t5.58321346448906e-08\t1.08872662557537e-06\n-TR24|c0_g1_i1\twt_GSNO\twt_ph8\t-2.16839334936064\t13.5222768601527\t3.73856822091501e-07\t4.86013868718952e-06\n-TR3788|c0_g1_i1\twt_GSNO\twt_ph8\t2.47096654484901\t13.0144557887788\t1.245732049043e-06\t9.71670998253539e-06\n-TR5075|c0_g1_i1\twt_GSNO\twt_ph8\t-3.68481140303272\t12.7944067233298\t3.44359702134355e-06\t2.23833806387331e-05\n-TR3854|c0_g1_i1\twt_GSNO\twt_ph8\t0.290746293924475\t17.7782076349597\t5.25322144866517e-07\t5.12189091244854e-06\n-TR1891|c0_g1_i1\twt_GSNO\twt_ph8\t-1.35768165107067\t14.6117632515968\t5.28666359293828e-06\t2.79053243123467e-05\n-TR4761|c0_g1_i1\twt_GSNO\twt_ph8\t-0.878920056028248\t14.8002262876656\t5.72416908971214e-06\t2.79053243123467e-05\n-TR2122|c0_g2_i2\twt_GSNO\twt_ph8\t-0.730166040402744\t14.7551588447381\t0.000213340170514583\t0.000924474072229861\n-TR3638|c0_g1_i1\twt_GSNO\twt_ph8\t-0.708321413581678\t14.6195575978943\t0.000258928735946659\t0.00100982207019197\n-TR2107|c1_g1_i1\twt_GSNO\twt_ph8\t1.90861736829884\t8.90712643491077\t0.00457979737107378\t0.0148843414559898\n-TR1678|c0_g1_i1\twt_GSNO\twt_ph8\t-2.86408187112217\t8.67828416118206\t0.00614682516189\t0.01844047548567\n-TR2278|c0_g1_i1\twt_GSNO\twt_ph8\t0.503051556783977\t15.2850549214884\t0.00155857674629228\t0.00552586300958173\n-TR1859|c3_g1_i1\twt_GSNO\twt_ph8\t-1.96144637998691\t6.77065030795652\t0.0428269385052548\t0.0982500353944082\n-TR2672|c0_g1_i1\twt_GSNO\twt_ph8\t-1.69730734417424\t8.97832173338033\t0.0866262290356731\t0.160877282494822\n-TR1479|c0_g1_i1\twt_GSNO\twt_ph8\t0.277933522953326\t15.1098597149167\t0.0157877120065803\t0.0439800548754737\n-TR1982|c2_g1_i1\twt_GSNO\twt_ph8\t-0.859948395691952\t9.74982883974683\t0.0845253825418736\t0.160877282494822\n-TR4859|c0_g1_i1\twt_GSNO\twt_ph8\t1.04376243585308\t7.84838377560073\t0.178339170085147\t0.289801151388364\n-TR2011|c5_g1_i1\twt_GSNO\twt_ph8\t0.835627288758852\t9.33803398810951\t0.117576176969539\t0.20843049553691\n-TR4084|c0_g1_i1\twt_GSNO\twt_ph8\t-0.383433512314591\t13.8345091917852\t0.0320674039619619\t0.083375250301101\n-TR1894|c2_g1_i1\twt_GSNO\twt_ph8\t0.899367664455804\t7.86698528437277\t0.236693956821629\t0.369242572641742\n-TR5212|c0_g1_i1\twt_GSNO\twt_ph8\t0.317453614519532\t13.3093804544918\t0.0408068910563242\t0.0982500353944082\n-TR2182|c3_g2_i6\twt_GSNO\twt_ph8\t-0.988859576038597\t7.34392475064937\t0.332144974966109\t0.462630500845651\n-TR3249|c0_g1_i1\twt_GSNO\twt_ph8\t-1.18548803762213\t8.36747688877935\t0.296376188714782\t0.444564283072173\n-TR1837|c2_g1_i1\twt_GSNO\twt_ph8\t0.83411458992077\t7.6102620160458\t0.393260306376011\t0.528867308574635\n-TR3807|c0_g1_i1\twt_GSNO\twt_ph8\t0.40219136988549\t5.09566487188118\t0.681998347783062\t0.765740423023185\n-TR4669|c0_g2_i1\twt_GSNO\twt_ph8\t6.05037553674292\t13.1239272719772\t0.480074268471172\t0.603964402270185\n+TR2779|c0_g1_i1\twt_GSNO\twt_ph8\t-2.23795519272236\t15.9076254017254\t2.92187316761747e-09\t1.13953053537081e-07\n+TR1492|c0_g1_i2\twt_GSNO\twt_ph8\t0.807554446371668\t16.8426446227048\t5.58321346449028e-08\t1.0887266255756e-06\n+TR24|c0_g1_i1\twt_GSNO\twt_ph8\t-2.16839334936065\t13.5222768601527\t3.73856822091552e-07\t4.86013868719017e-06\n+TR3788|c0_g1_i1\twt_GSNO\twt_ph8\t2.47096654484901\t13.0144557887788\t1.24573204904324e-06\t9.71670998253725e-06\n+TR5075|c0_g1_i1\twt_GSNO\twt_ph8\t-3.68481140303272\t12.7944067233298\t3.44359702134402e-06\t2.23833806387361e-05\n+TR3854|c0_g1_i1\twt_GSNO\twt_ph8\t0.290746293924475\t17.7782076349597\t5.253221448666e-07\t5.12189091244935e-06\n+TR1891|c0_g1_i1\twt_GSNO\twt_ph8\t-1.35768165107067\t14.6117632515968\t5.28666359293914e-06\t2.79053243123478e-05\n+TR4761|c0_g1_i1\twt_GSNO\twt_ph8\t-0.87892005602825\t14.8002262876656\t5.72416908971236e-06\t2.79053243123478e-05\n+TR2122|c0_g2_i2\twt_GSNO\twt_ph8\t-0.73016604040274\t14.7551588447381\t0.000213340170514584\t0.000924474072229863\n+TR3638|c0_g1_i1\twt_GSNO\twt_ph8\t-0.708321413581678\t14.6195575978943\t0.000258928735946679\t0.00100982207019205\n+TR2107|'..b'1736829884\t8.90712643491077\t0.00457979737107358\t0.0148843414559891\n+TR1678|c0_g1_i1\twt_GSNO\twt_ph8\t-2.86408187112217\t8.67828416118206\t0.00614682516188998\t0.01844047548567\n+TR2278|c0_g1_i1\twt_GSNO\twt_ph8\t0.503051556783975\t15.2850549214884\t0.00155857674629243\t0.00552586300958226\n+TR1859|c3_g1_i1\twt_GSNO\twt_ph8\t-1.96144637998691\t6.77065030795652\t0.0428269385052536\t0.0982500353944054\n+TR2672|c0_g1_i1\twt_GSNO\twt_ph8\t-1.69730734417424\t8.97832173338033\t0.0866262290356742\t0.160877282494824\n+TR1479|c0_g1_i1\twt_GSNO\twt_ph8\t0.277933522953328\t15.1098597149167\t0.0157877120065796\t0.0439800548754716\n+TR1982|c2_g1_i1\twt_GSNO\twt_ph8\t-0.859948395691952\t9.74982883974683\t0.0845253825418728\t0.160877282494824\n+TR4859|c0_g1_i1\twt_GSNO\twt_ph8\t1.04376243585308\t7.84838377560073\t0.178339170085145\t0.28980115138836\n+TR2011|c5_g1_i1\twt_GSNO\twt_ph8\t0.835627288758852\t9.33803398810951\t0.117576176969538\t0.208430495536908\n+TR4084|c0_g1_i1\twt_GSNO\twt_ph8\t-0.383433512314591\t13.8345091917852\t0.0320674039619627\t0.0833752503011029\n+TR1894|c2_g1_i1\twt_GSNO\twt_ph8\t0.899367664455804\t7.86698528437277\t0.236693956821627\t0.369242572641738\n+TR5212|c0_g1_i1\twt_GSNO\twt_ph8\t0.317453614519528\t13.3093804544918\t0.0408068910563263\t0.0982500353944054\n+TR2182|c3_g2_i6\twt_GSNO\twt_ph8\t-0.988859576038597\t7.34392475064937\t0.332144974966108\t0.46263050084565\n+TR3249|c0_g1_i1\twt_GSNO\twt_ph8\t-1.18548803762212\t8.36747688877935\t0.296376188714785\t0.444564283072177\n+TR1837|c2_g1_i1\twt_GSNO\twt_ph8\t0.83411458992077\t7.6102620160458\t0.39326030637601\t0.528867308574635\n+TR3807|c0_g1_i1\twt_GSNO\twt_ph8\t0.40219136988549\t5.09566487188118\t0.681998347783058\t0.765740423023183\n+TR4669|c0_g2_i1\twt_GSNO\twt_ph8\t6.05037553674292\t13.1239272719772\t0.480074268471177\t0.603964402270191\n TR1122|c0_g1_i1\twt_GSNO\twt_ph8\t0.184244267394782\t6.64199260311611\t0.869699168726351\t0.892585988955992\n-TR127|c1_g1_i1\twt_GSNO\twt_ph8\t-0.354388761220407\t7.15556768591471\t0.687202943738756\t0.765740423023185\n-TR2844|c0_g1_i1\twt_GSNO\twt_ph8\t0.251980888130202\t14.4425124782726\t0.0594765231313145\t0.128865800117848\n-TR2090|c0_g1_i1\twt_GSNO\twt_ph8\t-0.862128177746631\t9.64998833298881\t0.646749723219784\t0.764340581987017\n-TR3091|c0_g1_i1\twt_GSNO\twt_ph8\t0.148831558112849\t14.9878570236746\t0.0841354210369957\t0.160877282494822\n+TR127|c1_g1_i1\twt_GSNO\twt_ph8\t-0.354388761220407\t7.15556768591471\t0.687202943738754\t0.765740423023183\n+TR2844|c0_g1_i1\twt_GSNO\twt_ph8\t0.251980888130197\t14.4425124782726\t0.0594765231313182\t0.128865800117856\n+TR2090|c0_g1_i1\twt_GSNO\twt_ph8\t-0.862128177746631\t9.64998833298881\t0.646749723219787\t0.764340581987021\n+TR3091|c0_g1_i1\twt_GSNO\twt_ph8\t0.148831558112851\t14.9878570236746\t0.0841354210369898\t0.160877282494824\n TR5055|c0_g2_i1\twt_GSNO\twt_ph8\t0.0583511298028353\t9.18288041060754\t0.918331019801174\t0.918331019801174\n-TR4163|c0_g1_i1\twt_GSNO\twt_ph8\t0.161834057105857\t14.4879250602579\t0.126768900432688\t0.214955961603254\n-TR4277|c0_g1_i1\twt_GSNO\twt_ph8\t0.103273026252208\t13.9874746529507\t0.30829078508145\t0.445308911784317\n-TR939|c0_g1_i1\twt_GSNO\twt_ph8\t0.0333503331526365\t13.2856573711711\t0.715260879184748\t0.774865952450143\n-TR1449|c0_g1_i1\twt_GSNO\twt_ph8\t-0.049884213852527\t13.4293306544833\t0.75234222467997\t0.793009371959969\n-TR2487|c0_g1_i1\twt_GSNO\twt_ph8\t0.0480185034754555\t16.5239765307922\t0.407818984620182\t0.530164680006236\n-TR131|c0_g1_i1\twt_GSNO\twt_ph8\t0.0203187870937255\t17.0810493411762\t0.539920494505425\t0.658028102678487\n+TR4163|c0_g1_i1\twt_GSNO\twt_ph8\t0.161834057105863\t14.4879250602579\t0.126768900432678\t0.214955961603237\n+TR4277|c0_g1_i1\twt_GSNO\twt_ph8\t0.103273026252208\t13.9874746529507\t0.308290785081446\t0.445308911784311\n+TR939|c0_g1_i1\twt_GSNO\twt_ph8\t0.0333503331526316\t13.2856573711711\t0.71526087918478\t0.774865952450178\n+TR1449|c0_g1_i1\twt_GSNO\twt_ph8\t-0.049884213852527\t13.4293306544833\t0.752342224679971\t0.793009371959969\n+TR2487|c0_g1_i1\twt_GSNO\twt_ph8\t0.0480185034754555\t16.5239765307922\t0.407818984620183\t0.530164680006237\n+TR131|c0_g1_i1\twt_GSNO\twt_ph8\t0.0203187870937285\t17.0810493411762\t0.539920494505375\t0.658028102678426\n' |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf |
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| diff -r 3f4094b6a565 -r c0096052b35b test-data/filtered/Trinity_filtered_exp.fasta --- a/test-data/filtered/Trinity_filtered_exp.fasta Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_exp.fasta Tue Apr 11 19:55:15 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ ->TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA max_expr_any=222.00 CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT @@ -6,12 +6,12 @@ GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG TATATGGTACAGATGTAAAG ->TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA max_expr_any=1094.00 AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC ->TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA max_expr_any=65.00 GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT @@ -22,12 +22,12 @@ CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT G ->TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA max_expr_any=425.00 GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC ATACATGATTCTATTCAACCAA ->TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:0 pct_iso_expr=NA pct_dom_iso_expr=NA max_expr_any=36.00 ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/filtered/Trinity_filtered_hi_iso.fasta --- a/test-data/filtered/Trinity_filtered_hi_iso.fasta Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta Tue Apr 11 19:55:15 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ ->TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any= CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT @@ -6,18 +6,18 @@ GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG TATATGGTACAGATGTAAAG ->TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any= AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC ->TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any= TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA ->TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any= GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT @@ -28,17 +28,17 @@ CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT G ->TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any= ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC ->TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any= GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC ATACATGATTCTATTCAACCAA ->TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any= ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA |
| b |
| diff -r 3f4094b6a565 -r c0096052b35b test-data/filtered/Trinity_filtered_pct_iso.fasta --- a/test-data/filtered/Trinity_filtered_pct_iso.fasta Sun Dec 19 16:21:54 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta Tue Apr 11 19:55:15 2023 +0000 |
| [ |
| @@ -1,4 +1,4 @@ ->TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN1_c0_g1_i1 len=380 path=[358:0-379] [-1, 358, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any=222.00 CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGG CTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGC AAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTT @@ -6,18 +6,18 @@ GGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATG AAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATG TATATGGTACAGATGTAAAG ->TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN0_c0_g1_i1 len=229 path=[207:0-228] [-1, 207, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any=1094.00 AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGT TTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCT ACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTA TAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC ->TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c0_g1_i1 len=279 path=[257:0-278] [-1, 257, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any=23.00 TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGA ACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACC AAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAG AGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGA AAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA ->TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c1_g1_i1 len=541 path=[519:0-540] [-1, 519, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any=65.00 GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTAT TCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGA TGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTT @@ -28,17 +28,17 @@ CCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTG GTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGT G ->TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c2_g1_i1 len=240 path=[218:0-239] [-1, 218, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any=11.00 ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGA GTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGC TACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTG TTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC ->TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN2_c3_g1_i1 len=202 path=[180:0-201] [-1, 180, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any=425.00 GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTC AAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCC CCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGAC ATACATGATTCTATTCAACCAA ->TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 +>TRINITY_DN3_c0_g1_i1 len=216 path=[194:0-215] [-1, 194, -2] top_iso:1 pct_iso_expr=100 pct_dom_iso_expr=100 max_expr_any=36.00 ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATG CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA |