| Previous changeset 17:e3b16fd7dd08 (2021-12-19) Next changeset 19:3b36efd62b3e (2023-08-08) |
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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:
describe_samples.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 e3b16fd7dd08 -r 57f477b57c35 describe_samples.xml --- a/describe_samples.xml Sun Dec 19 16:24:50 2021 +0000 +++ b/describe_samples.xml Tue Apr 11 19:56:55 2023 +0000 |
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| @@ -1,12 +1,11 @@ -<?xml version="1.0"?> -<tool id="describe_samples" name="Describe samples" version="@WRAPPER_VERSION@"> +<tool id="describe_samples" name="Describe samples" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>and replicates</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> <command detect_errors="aggressive"><![CDATA[ - cp $sample_list $output + mv '$sample_list' '$output' ]]></command> <configfiles> <configfile name="sample_list"><![CDATA[#for $sample in $samples: @@ -15,8 +14,8 @@ </configfiles> <inputs> <repeat name="samples" title="Samples"> - <param name="name" type="text" label="Full sample name" help="e.g. CondA_replicate1" optional="False" /> - <param name="condition" type="text" label="Condition" help="e.g. ConditionA" optional="False" /> + <param name="name" type="text" label="Full sample name" help="e.g. CondA_replicate1" /> + <param name="condition" type="text" label="Condition" help="e.g. ConditionA" /> </repeat> </inputs> <outputs> @@ -62,7 +61,7 @@ ConditionC CondC_replicate3 =========== ================ - IThe output file can be used in the tools 'RNASeq samples quality check for transcript quantification' and 'Differential expression analysis'. + The output file can be used in the tools 'RNASeq samples quality check for transcript quantification' and 'Differential expression analysis'. The names in column 2 must match the names given to the datasets in your history. ]]></help> <expand macro="citation"/> |
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| diff -r e3b16fd7dd08 -r 57f477b57c35 macros.xml --- a/macros.xml Sun Dec 19 16:24:50 2021 +0000 +++ b/macros.xml Tue Apr 11 19:56:55 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 e3b16fd7dd08 -r 57f477b57c35 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix Tue Apr 11 19:56:55 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix Tue Apr 11 19:56:55 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Tue Apr 11 19:56:55 2023 +0000 |
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| 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 e3b16fd7dd08 -r 57f477b57c35 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Tue Apr 11 19:56:55 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Tue Apr 11 19:56:55 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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| diff -r e3b16fd7dd08 -r 57f477b57c35 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Sun Dec 19 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Tue Apr 11 19:56:55 2023 +0000 |
| 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 e3b16fd7dd08 -r 57f477b57c35 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Tue Apr 11 19:56:55 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Tue Apr 11 19:56:55 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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| diff -r e3b16fd7dd08 -r 57f477b57c35 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Sun Dec 19 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Tue Apr 11 19:56:55 2023 +0000 |
| b |
| 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 e3b16fd7dd08 -r 57f477b57c35 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Tue Apr 11 19:56:55 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 |
| b |
| diff -r e3b16fd7dd08 -r 57f477b57c35 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf |
| b |
| 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 e3b16fd7dd08 -r 57f477b57c35 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 16:24:50 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Tue Apr 11 19:56:55 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 e3b16fd7dd08 -r 57f477b57c35 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf |
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| b |
| diff -r e3b16fd7dd08 -r 57f477b57c35 test-data/filtered/Trinity_filtered_exp.fasta --- a/test-data/filtered/Trinity_filtered_exp.fasta Sun Dec 19 16:24:50 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_exp.fasta Tue Apr 11 19:56:55 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 e3b16fd7dd08 -r 57f477b57c35 test-data/filtered/Trinity_filtered_hi_iso.fasta --- a/test-data/filtered/Trinity_filtered_hi_iso.fasta Sun Dec 19 16:24:50 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta Tue Apr 11 19:56:55 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 e3b16fd7dd08 -r 57f477b57c35 test-data/filtered/Trinity_filtered_pct_iso.fasta --- a/test-data/filtered/Trinity_filtered_pct_iso.fasta Sun Dec 19 16:24:50 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta Tue Apr 11 19:56:55 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 |