Mercurial > repos > iuc > trinity_run_de_analysis
changeset 20:c63338cf419f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70
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--- a/macros.xml Sun Dec 19 16:19:00 2021 +0000 +++ b/macros.xml Tue Apr 11 19:51:53 2023 +0000 @@ -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>
--- a/run_de_analysis.xml Sun Dec 19 16:19:00 2021 +0000 +++ b/run_de_analysis.xml Tue Apr 11 19:51:53 2023 +0000 @@ -1,30 +1,21 @@ -<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@WRAPPER_VERSION@"> +<tool id="trinity_run_de_analysis" name="Differential expression analysis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05"> <description>using a Trinity assembly</description> <macros> <import>macros.xml</import> </macros> <expand macro="bio_tools"/> - <expand macro="requirements"> - <requirement type="package" version="3.20.7">bioconductor-edger</requirement> - <requirement type="package" version="3.34.9">bioconductor-limma</requirement> - <requirement type="package" version="1.18.1">bioconductor-deseq2</requirement> - </expand> + <expand macro="requirements"/> <command detect_errors="aggressive"><![CDATA[ - ln -f -s '${matrix}' "input.matrix" - + ln -f -s '${matrix}' input.matrix && - run_DE_analysis.pl - - --matrix "input.matrix" - - --samples_file '${samples}' - + --matrix input.matrix + --samples_file '${samples_file}' --method ${method_choice.method} #if $method_choice.method == "edgeR": - --dispersion ${method_choice.edger_dispersion} + --dispersion ${method_choice.dispersion} #end if #if $method_choice.method == "ROTS": @@ -46,34 +37,32 @@ ]]></command> <inputs> - <param format="tabular" name="matrix" argument="--matrix" type="data" label="Expression matrix" help="output of Build expression matrix - matrix of raw read counts (not normalized!)"/> - <param format="tabular" name="samples" argument="--samples_file" type="data" label="Sample description" help="file describing samples and replicates"/> + <param argument="--matrix" format="tabular" type="data" label="Expression matrix" help="output of Build expression matrix - matrix of raw read counts (not normalized!)"/> + <param argument="--samples_file" format="tabular" type="data" label="Sample description" help="file describing samples and replicates"/> <conditional name="method_choice"> - <param type="select" name="method" argument="--method" label="Differential analysis method"> + <param type="select" argument="--method" label="Differential analysis method"> <option value="edgeR">edgeR</option> <option value="DESeq2">DESeq2</option> <option value="voom">voom</option> <option value="ROTS">ROTS</option> </param> <when value="edgeR"> - <param name="edger_dispersion" argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" /> + <param argument="--dispersion" type="float" value="0.1" label="edgeR dispersion value" help="Read edgeR manual to guide your value choice" /> </when> <when value="ROTS"> - <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="number of bootstraps and permutation resampling" /> - <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="largest top genes size" /> + <param name="rots_b" argument="--ROTS_B" type="integer" value="500" label="Number of bootstraps and permutation resampling" /> + <param name="rots_k" argument="--ROTS_K" type="integer" value="5000" label="Largest top genes size" /> </when> - <when value="voom"> - </when> - <when value="DESeq2"> - </when> + <when value="voom"/> + <when value="DESeq2" /> </conditional> <section name="additional_params" title="Additional Options" expanded="False"> <param name="min_cpm" type="integer" value="1" label="Minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/> <param name="min_reps" type="integer" value="2" label="Minimum number of replicates meeting minimum count per replicate" help="Only those rows of matrix meeting requirement will be tested"/> - <param name="reference_sample" argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/> - <param format="tabular" name="contrasts" argument="--contrasts" optional="true" type="data" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/> + <param argument="--reference_sample" type="text" optional="true" value="" label="Name of a sample to which all other samples should be compared" help="default is doing all pairwise-comparisons among samples"/> + <param argument="--contrasts" optional="true" type="data" format="tabular" label="Pairs of sample comparisons to perform" help="A 2-column tabular with lists of pairs of samples to compare"/> </section> </inputs> <outputs> @@ -90,7 +79,7 @@ <tests> <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> - <param name="samples" value="count/samples.txt"/> + <param name="samples_file" value="count/samples.txt"/> <param name="method" value="DESeq2"/> <output_collection name="DE_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.DESeq2" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results"/> @@ -110,7 +99,7 @@ </test> <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> - <param name="samples" value="count/samples.txt"/> + <param name="samples_file" value="count/samples.txt"/> <param name="method" value="edgeR"/> <output_collection name="DE_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.edgeR" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results"/> @@ -130,7 +119,7 @@ </test> <test> <param name="matrix" value="count/qcheck/matrix.counts.matrix"/> - <param name="samples" value="count/samples.txt"/> + <param name="samples_file" value="count/samples.txt"/> <param name="method" value="voom"/> <output_collection name="DE_results"> <element name="input.matrix.wt_37_vs_wt_GSNO.voom" compare="sim_size" file="count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results"/>
--- a/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix Tue Apr 11 19:51:53 2023 +0000 @@ -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
--- a/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix Tue Apr 11 19:51:53 2023 +0000 @@ -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
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -1,38 +1,38 @@ sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR4277|c0_g1_i1 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57661492404411 0.121615845393926 37.6317321909822 0 0 -TR131|c0_g1_i1 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.68565819121436 0.188173369545147 -30.2149990987446 1.50487696827007e-200 2.48304699764561e-199 -TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.09227622940716 0.143766888218038 21.5089598706302 1.28350063536341e-102 1.41185069889975e-101 -TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.30529554105297 0.242003292489129 -17.790235400398 8.41257542125902e-71 6.94037472253869e-70 -TR3638|c0_g1_i1 wt_37 wt_GSNO 583.00358519031 183.754416330029 383.37900076017 1.66225356244238 0.144704273829595 11.487245804501 1.5290952692426e-30 1.00920287770012e-29 -TR2487|c0_g1_i1 wt_37 wt_GSNO 342.210853400436 920.407318992504 631.30908619647 -1.42823125318501 0.124766100464837 -11.44727011475 2.42667678803784e-30 1.33467223342081e-29 -TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.78185518936858 0.26452057618315 -10.5165928091827 7.24461724546031e-26 3.41531955857415e-25 -TR1479|c0_g1_i1 wt_37 wt_GSNO 129.593534475689 371.064629188207 250.329081831948 -1.51632040995179 0.145721574162902 -10.405599985193 2.33778717307793e-25 9.64337208894648e-25 -TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.72565745131165 0.439033221898883 6.20831708252687 5.35550100392654e-10 1.96368370143973e-09 -TR3854|c0_g1_i1 wt_37 wt_GSNO 1573.69549271337 2374.56159860719 1974.12854566028 -0.593952181868433 0.11125243839418 -5.33877900063632 9.35746226940931e-08 3.08796254890507e-07 -TR2122|c0_g2_i2 wt_37 wt_GSNO 119.534640490118 199.143666337033 159.339153413576 -0.73989736621081 0.168946597067547 -4.37947481070002 1.18965671308434e-05 3.56897013925302e-05 -TR1449|c0_g1_i1 wt_37 wt_GSNO 180.814952011467 104.755290736358 142.785121373912 0.785811747593425 0.186397685526418 4.2157806057203 2.48915666101662e-05 6.6882655779165e-05 -TR4163|c0_g1_i1 wt_37 wt_GSNO 347.283468916919 232.772947466212 290.028208191566 0.5773903092812 0.137377906430929 4.20293425836637 2.63477128827014e-05 6.6882655779165e-05 -TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.9857084616452 0.761209385049731 3.92232218924907 8.76996107235725e-05 0.000206720510991278 -TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.08513896568298 0.577312677901881 3.61180179389265 0.00030407694239889 0.000668969273277559 -TR2844|c0_g1_i1 wt_37 wt_GSNO 158.206282615139 231.762548186068 194.984415400603 -0.551426184671915 0.155135532159318 -3.55448024702441 0.000378726959348647 0.000781124353656584 -TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.52517488060096 1.00261297574214 3.51598769005717 0.00043812129728732 0.000850470753557739 -TR5212|c0_g1_i1 wt_37 wt_GSNO 65.7079302129484 107.875371765755 86.7916509893515 -0.715754705745061 0.210644233010842 -3.39793164766215 0.000678973819799399 0.0012447853362989 -TR1894|c2_g1_i1 wt_37 wt_GSNO 13.3497721959996 2.96749216411516 8.15863218005739 2.116499695166 0.744618031030184 2.84239651333424 0.00447757649596373 0.00777684338772647 -TR24|c0_g1_i1 wt_37 wt_GSNO 69.9065207344592 41.2394742844514 55.5729975094553 0.763675526543044 0.270944643994893 2.81856660933825 0.00482386011442888 0.00795936918880766 +TR4277|c0_g1_i1 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57661492404411 0.121615845393921 37.6317321909836 0 0 +TR131|c0_g1_i1 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.68565819121436 0.188173369545145 -30.214999098745 1.5048769682518e-200 2.48304699761546e-199 +TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.09227622940716 0.143766888218033 21.5089598706309 1.28350063534336e-102 1.41185069887769e-101 +TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.30529554105297 0.242003292489129 -17.790235400398 8.41257542126328e-71 6.94037472254221e-70 +TR3638|c0_g1_i1 wt_37 wt_GSNO 583.00358519031 183.754416330029 383.37900076017 1.66225356244238 0.144704273829591 11.4872458045013 1.52909526923641e-30 1.00920287769603e-29 +TR2487|c0_g1_i1 wt_37 wt_GSNO 342.210853400436 920.407318992504 631.30908619647 -1.42823125318502 0.124766100464834 -11.4472701147503 2.42667678802884e-30 1.33467223341586e-29 +TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.78185518936858 0.264520576183151 -10.5165928091826 7.24461724546331e-26 3.41531955857556e-25 +TR1479|c0_g1_i1 wt_37 wt_GSNO 129.593534475689 371.064629188207 250.329081831948 -1.5163204099518 0.145721574162894 -10.4055999851936 2.33778717306381e-25 9.6433720888882e-25 +TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.72565745131165 0.439033221898883 6.20831708252687 5.35550100392651e-10 1.96368370143972e-09 +TR3854|c0_g1_i1 wt_37 wt_GSNO 1573.69549271337 2374.56159860719 1974.12854566028 -0.593952181868431 0.11125243839418 -5.33877900063628 9.3574622694111e-08 3.08796254890566e-07 +TR2122|c0_g2_i2 wt_37 wt_GSNO 119.534640490118 199.143666337033 159.339153413576 -0.739897366210811 0.168946597067543 -4.37947481070013 1.18965671308372e-05 3.56897013925116e-05 +TR1449|c0_g1_i1 wt_37 wt_GSNO 180.814952011467 104.755290736358 142.785121373912 0.785811747593426 0.186397685526415 4.21578060572037 2.48915666101586e-05 6.68826557791634e-05 +TR4163|c0_g1_i1 wt_37 wt_GSNO 347.283468916919 232.772947466212 290.028208191566 0.577390309281198 0.137377906430928 4.20293425836637 2.63477128827007e-05 6.68826557791634e-05 +TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.9857084616452 0.76120938504973 3.92232218924907 8.76996107235725e-05 0.000206720510991278 +TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.08513896568298 0.577312677901881 3.61180179389265 0.000304076942398887 0.000668969273277552 +TR2844|c0_g1_i1 wt_37 wt_GSNO 158.206282615139 231.762548186068 194.984415400603 -0.551426184671918 0.155135532159314 -3.55448024702451 0.000378726959348502 0.000781124353656284 +TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.52517488060096 1.00261297574214 3.51598769005718 0.000438121297287318 0.000850470753557735 +TR5212|c0_g1_i1 wt_37 wt_GSNO 65.7079302129484 107.875371765755 86.7916509893515 -0.715754705745063 0.210644233010843 -3.39793164766215 0.000678973819799395 0.00124478533629889 +TR1894|c2_g1_i1 wt_37 wt_GSNO 13.3497721959996 2.96749216411516 8.15863218005739 2.116499695166 0.744618031030184 2.84239651333424 0.00447757649596375 0.00777684338772651 +TR24|c0_g1_i1 wt_37 wt_GSNO 69.9065207344592 41.2394742844514 55.5729975094553 0.763675526543045 0.270944643994892 2.81856660933826 0.00482386011442872 0.00795936918880738 TR4669|c0_g2_i1 wt_37 wt_GSNO 0 167.096667347181 83.5483336735905 -10.0466852501689 3.90738405199054 -2.57120495873725 0.0101345328521317 0.0159256944819212 -TR2779|c0_g1_i1 wt_37 wt_GSNO 155.915506826481 205.619872596257 180.767689711369 -0.403209397282846 0.18950756245476 -2.12766916559914 0.033364523163095 0.0500467847446426 -TR3807|c0_g1_i1 wt_37 wt_GSNO 3.48709246029019 0.350050334268211 1.9185713972792 3.04810928058763 1.5874506366217 1.92012854464212 0.0548416645360559 0.0786858665082542 -TR1492|c0_g1_i2 wt_37 wt_GSNO 1640.89375005483 1435.64893261411 1538.27134133447 0.192601921423703 0.101311986688049 1.90107733270247 0.0572918841322824 0.0787763406818883 -TR4084|c0_g1_i1 wt_37 wt_GSNO 93.2264707954139 121.352438036668 107.289454416041 -0.381231151484282 0.21399248813321 -1.78151651401411 0.0748281095286258 0.0987731045777861 -TR1891|c0_g1_i1 wt_37 wt_GSNO 107.628573623499 135.399287466928 121.513930545214 -0.329513668205708 0.189733845104182 -1.7367152814764 0.0824374390602291 0.104632134191829 -TR1837|c2_g1_i1 wt_37 wt_GSNO 0.308903905435236 2.22601224010275 1.26745807276899 -2.87715913917267 1.7927876855897 -1.60485213184979 0.108526350064413 1 -TR5075|c0_g1_i1 wt_37 wt_GSNO 15.8633018853512 9.23822794034992 12.5507649128506 0.776103293030194 0.516446682273215 1.5027752518693 0.13289700980576 0.16070937436521 -TR4859|c0_g1_i1 wt_37 wt_GSNO 7.32690480813971 3.17910584569163 5.25300532691567 1.23041974278822 0.82607009598701 1.48948587869905 0.13635946915836 0.16070937436521 -TR939|c0_g1_i1 wt_37 wt_GSNO 84.2568220960088 96.9171174594069 90.5869697777078 -0.203187486812458 0.203052234052517 -1.00066609835923 0.316988262617008 0.354139456794138 -TR2278|c0_g1_i1 wt_37 wt_GSNO 486.5272515724 448.140178813055 467.333715192727 0.118924512672215 0.120068895863502 0.990468945491189 0.321944960721944 0.354139456794138 -TR2011|c5_g1_i1 wt_37 wt_GSNO 5.60408627995835 7.88255079488408 6.74331853742122 -0.50342873702063 0.712267625142964 -0.706797163383052 0.479692537619295 0.510640443272153 -TR2182|c3_g2_i6 wt_37 wt_GSNO 2.24974854180929 1.3031439398571 1.77644624083319 0.878491642458712 1.45214866443311 0.604959852923637 0.545205672528741 0.562243349795264 +TR2779|c0_g1_i1 wt_37 wt_GSNO 155.915506826481 205.619872596257 180.767689711369 -0.403209397282847 0.189507562454757 -2.12766916559918 0.0333645231630914 0.0500467847446371 +TR3807|c0_g1_i1 wt_37 wt_GSNO 3.48709246029019 0.350050334268211 1.9185713972792 3.04810928058763 1.5874506366217 1.92012854464212 0.054841664536056 0.0786858665082543 +TR1492|c0_g1_i2 wt_37 wt_GSNO 1640.89375005483 1435.64893261411 1538.27134133447 0.192601921423702 0.101311986688034 1.90107733270273 0.0572918841322478 0.0787763406818408 +TR4084|c0_g1_i1 wt_37 wt_GSNO 93.2264707954139 121.352438036668 107.289454416041 -0.381231151484283 0.213992488133209 -1.78151651401413 0.0748281095286238 0.0987731045777834 +TR1891|c0_g1_i1 wt_37 wt_GSNO 107.628573623499 135.399287466928 121.513930545214 -0.329513668205707 0.189733845104182 -1.73671528147639 0.0824374390602302 0.104632134191831 +TR1837|c2_g1_i1 wt_37 wt_GSNO 0.308903905435236 2.22601224010275 1.26745807276899 -2.87715913917267 1.7927876855897 -1.60485213184978 0.108526350064413 1 +TR5075|c0_g1_i1 wt_37 wt_GSNO 15.8633018853512 9.23822794034992 12.5507649128506 0.776103293030194 0.516446682273216 1.5027752518693 0.132897009805761 0.160709374365211 +TR4859|c0_g1_i1 wt_37 wt_GSNO 7.32690480813971 3.17910584569163 5.25300532691567 1.23041974278822 0.82607009598701 1.48948587869905 0.136359469158361 0.160709374365211 +TR939|c0_g1_i1 wt_37 wt_GSNO 84.2568220960088 96.9171174594069 90.5869697777078 -0.203187486812456 0.203052234052516 -1.00066609835922 0.316988262617012 0.35413945679411 +TR2278|c0_g1_i1 wt_37 wt_GSNO 486.5272515724 448.140178813055 467.333715192727 0.118924512672213 0.120068895863495 0.990468945491242 0.321944960721918 0.35413945679411 +TR2011|c5_g1_i1 wt_37 wt_GSNO 5.60408627995835 7.88255079488408 6.74331853742122 -0.503428737020628 0.712267625142964 -0.70679716338305 0.479692537619297 0.510640443272154 +TR2182|c3_g2_i6 wt_37 wt_GSNO 2.24974854180929 1.3031439398571 1.77644624083319 0.878491642458711 1.45214866443311 0.604959852923636 0.545205672528742 0.562243349795265 TR3249|c0_g1_i1 wt_37 wt_GSNO 1.12573841927462 2.128954842887 1.62734663108081 -0.858277190977929 1.45820967054459 -0.588582841216099 0.556141147160533 1 TR1678|c0_g1_i1 wt_37 wt_GSNO 0.595141051681226 0.700100668536423 0.647620860108824 -0.322353878735801 2.26929239960538 -0.142050393678601 0.887040200834538 1 -TR1122|c0_g1_i1 wt_37 wt_GSNO 1.41370386226057 1.3031439398571 1.35842390105883 0.189589394350501 1.67633508161709 0.113097552171736 0.909953215626095 1 -TR1982|c2_g1_i1 wt_37 wt_GSNO 5.73684100209948 5.71221669652109 5.72452884931028 -0.0104554076697487 0.738553450989727 -0.0141566025529196 0.988705042660126 0.988705042660126 +TR1122|c0_g1_i1 wt_37 wt_GSNO 1.41370386226057 1.3031439398571 1.35842390105883 0.1895893943505 1.67633508161709 0.113097552171736 0.909953215626095 1 +TR1982|c2_g1_i1 wt_37 wt_GSNO 5.73684100209948 5.71221669652109 5.72452884931028 -0.0104554076697489 0.738553450989728 -0.0141566025529198 0.988705042660126 0.988705042660126
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -1,39 +1,39 @@ sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR4277|c0_g1_i1 wt_37 wt_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.85332629705957 0.130960775627329 37.0593887659196 1.26787233139066e-300 4.81791485928452e-299 -TR131|c0_g1_i1 wt_37 wt_ph8 32.0461070493257 1436.30905989883 734.177583474076 -5.49708942597102 0.198466854292743 -27.6977707212645 7.42748041559505e-169 1.41122127896306e-167 -TR3091|c0_g1_i1 wt_37 wt_ph8 20.4914097091341 321.651020117047 171.071214913091 -3.98630633515117 0.247421953542878 -16.1113687693051 2.12272588309166e-58 2.47056970916163e-57 -TR4761|c0_g1_i1 wt_37 wt_ph8 2012.6141923276 384.620292965437 1198.61724264652 2.3876556238738 0.148312557773369 16.0988095662291 2.60059969385434e-58 2.47056970916163e-57 -TR5075|c0_g1_i1 wt_37 wt_ph8 19.3833722195684 136.98672801182 78.1850501156942 -2.81556781738656 0.271397918695418 -10.3743161735385 3.24527446090745e-25 2.46640859028966e-24 -TR2779|c0_g1_i1 wt_37 wt_ph8 191.51955185349 1058.15934185376 624.839446853626 -2.46872482043468 0.248047686960726 -9.95262181511717 2.45625242439133e-23 1.55562653544784e-22 -TR1891|c0_g1_i1 wt_37 wt_ph8 131.416087212132 376.595292171713 254.005689691923 -1.51763504949468 0.1638333296262 -9.26328637132193 1.98234808919548e-20 1.07613181984897e-19 -TR1492|c0_g1_i2 wt_37 wt_ph8 2006.11782336441 890.823502721036 1448.47066304272 1.17138763330801 0.12740597231583 9.19413440371721 3.78025797563847e-20 1.79562253842827e-19 -TR2487|c0_g1_i1 wt_37 wt_ph8 418.818667162757 965.862817209246 692.340742186001 -1.2068861494209 0.138672539999103 -8.70313725722989 3.22833072204789e-18 1.36307297153133e-17 -TR3638|c0_g1_i1 wt_37 wt_ph8 713.131183384274 326.063958913919 519.597571149096 1.12959116050602 0.141514345090045 7.98216717737888 1.43786102301427e-15 5.46387188745423e-15 -TR2122|c0_g2_i2 wt_37 wt_ph8 146.135958637131 360.821667264163 253.478812950647 -1.30611123021679 0.169971549866392 -7.68429323168187 1.53843927144304e-14 5.31460839225778e-14 -TR2107|c1_g1_i1 wt_37 wt_ph8 59.5986596731862 1.89840873462066 30.7485342039034 4.94663101068376 0.648801734442531 7.62425676148051 2.45444399373987e-14 7.77240598017624e-14 -TR1479|c0_g1_i1 wt_37 wt_ph8 158.005105094407 334.827472148091 246.416288621249 -1.08064044509537 0.1658526880096 -6.5156643408325 7.23686413447617e-11 2.11539105469303e-10 -TR24|c0_g1_i1 wt_37 wt_ph8 85.6614643869141 199.923709280262 142.792586833588 -1.2309601921531 0.197065470330035 -6.24645296860761 4.19878369504606e-10 1.13966986008393e-09 -TR4163|c0_g1_i1 wt_37 wt_ph8 424.593720981574 227.471218917767 326.03246994967 0.902378343080323 0.156120482680011 5.78001251078543 7.46950706226027e-09 1.89227512243927e-08 -TR1449|c0_g1_i1 wt_37 wt_ph8 220.782434528097 117.26089394399 169.021664236043 0.916182468982544 0.175267159439457 5.22734819182726 1.71958482582468e-07 4.0840139613336e-07 -TR2278|c0_g1_i1 wt_37 wt_ph8 594.657329919233 348.341653317169 471.499491618201 0.77372548280461 0.158144801146882 4.8925129197639 9.95565784679233e-07 2.22538234222417e-06 -TR5055|c0_g2_i1 wt_37 wt_ph8 28.6665933385886 6.05959103586122 17.3630921872249 2.22056293047175 0.515653625436263 4.30630722045843 1.66002467176804e-05 3.50449652928809e-05 -TR127|c1_g1_i1 wt_37 wt_ph8 16.3791628279609 1.58772512712498 8.98344397754296 3.35782864860774 0.805715621214412 4.16751091848842 3.07943766984562e-05 6.15887533969124e-05 -TR1894|c2_g1_i1 wt_37 wt_ph8 16.2826445742552 1.67571344127509 8.97917900776516 3.31835899440704 0.806156235895963 4.1162728099709 3.85048512190331e-05 7.31592173161629e-05 -TR2672|c0_g1_i1 wt_37 wt_ph8 22.3129914439134 7.89947501226409 15.1062332280887 1.4879160019133 0.490304786216723 3.03467566244728 0.00240794483755529 0.00435723351557623 -TR4084|c0_g1_i1 wt_37 wt_ph8 113.2594381118 173.837287636503 143.548362874151 -0.610546095515356 0.203809508378262 -2.99567032163292 0.00273842322103228 0.00473000374541939 -TR4859|c0_g1_i1 wt_37 wt_ph8 8.91205730249659 1.28188505334354 5.09697117792006 2.79846628921536 0.943303749490582 2.96666507551426 0.00301048704228202 0.00497384815681378 -TR1678|c0_g1_i1 wt_37 wt_ph8 0.738899982352077 7.85275634721875 4.29582816478541 -3.47431884008145 1.21198503063676 -2.8666351087324 0.00414861034620894 0.00656863304816415 -TR3807|c0_g1_i1 wt_37 wt_ph8 4.23896204531587 0.352255997713617 2.29560902151474 3.60257127355045 1.494771199452 2.41011552461754 0.0159474699414718 0.0242401543110371 -TR1859|c3_g1_i1 wt_37 wt_ph8 0.361569353912422 2.25550826604853 1.30853880998047 -2.58650633406891 1.68391965639604 -1.53600340980911 0.124537544060973 0.181135380859875 -TR3249|c0_g1_i1 wt_37 wt_ph8 1.36481976577862 4.37661229401476 2.87071602989669 -1.67837058189371 1.10474169040967 -1.51924254915312 0.12870145482149 0.181135380859875 -TR2090|c0_g1_i1 wt_37 wt_ph8 0 5.87877087384675 2.93938543692337 -4.93100736412614 3.57047444665656 -1.38105101655149 0.167263275059569 0.227000159009415 -TR1982|c2_g1_i1 wt_37 wt_ph8 7.00144976454503 11.520013112092 9.26073143831853 -0.727260398375603 0.567300823658434 -1.28196605406919 0.199854554547715 0.261878381821143 -TR1837|c2_g1_i1 wt_37 wt_ph8 0.377330628439655 1.67813520813222 1.02773291828594 -2.14007669057536 1.85335822648042 -1.15470212935543 0.248212427250959 0.314402407851215 -TR5212|c0_g1_i1 wt_37 wt_ph8 80.2050001877881 94.8352723753388 87.5201362815635 -0.236625075567938 0.21614403033503 -1.09475646956875 0.273623341840838 0.335409257740381 -TR3854|c0_g1_i1 wt_37 wt_ph8 1925.26464813324 2107.16376011081 2016.21420412203 -0.130625245556183 0.13088163358419 -0.998041069468758 0.318259444082768 0.377933089848287 -TR2844|c0_g1_i1 wt_37 wt_ph8 193.030766468894 213.82243412349 203.426600296192 -0.144061748535941 0.17173092225162 -0.838880654963596 0.401536284440308 0.450271927171228 -TR1122|c0_g1_i1 wt_37 wt_ph8 1.69354093201913 0.660517838352177 1.17702938518565 1.3946217378633 1.66721495733336 0.836497856337578 0.402874882205836 0.450271927171228 -TR2011|c5_g1_i1 wt_37 wt_ph8 6.84875389533898 4.81927837273561 5.8340161340373 0.48395696149425 0.739237535887472 0.654670438120067 0.512679962329315 0.556623959100399 -TR2182|c3_g2_i6 wt_37 wt_ph8 2.76248771922916 1.94482465855284 2.353656188891 0.516404389322083 1.10366040723297 0.467901526536393 0.63985501178297 0.675402512437579 -TR3788|c0_g1_i1 wt_37 wt_ph8 23.7579432209456 26.0024682525169 24.8802057367313 -0.125340757750783 0.352879389384874 -0.355194328490741 0.722444013290729 0.741969527163451 -TR939|c0_g1_i1 wt_37 wt_ph8 103.002135647151 102.820214322362 102.911174984756 0.000973457550309434 0.195891269167835 0.00496937691222674 0.996035027203904 0.996035027203904 +TR4277|c0_g1_i1 wt_37 wt_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.85332629705957 0.130960775627329 37.0593887659196 1.26787233139334e-300 4.81791485929468e-299 +TR131|c0_g1_i1 wt_37 wt_ph8 32.0461070493257 1436.30905989883 734.177583474076 -5.49708942597102 0.198466854292742 -27.6977707212647 7.42748041554821e-169 1.41122127895416e-167 +TR3091|c0_g1_i1 wt_37 wt_ph8 20.4914097091341 321.651020117047 171.071214913091 -3.98630633515117 0.247421953542881 -16.1113687693049 2.12272588309764e-58 2.47056970915936e-57 +TR4761|c0_g1_i1 wt_37 wt_ph8 2012.6141923276 384.620292965437 1198.61724264652 2.38765562387381 0.148312557773368 16.0988095662291 2.60059969385195e-58 2.47056970915936e-57 +TR5075|c0_g1_i1 wt_37 wt_ph8 19.3833722195684 136.98672801182 78.1850501156942 -2.81556781738656 0.271397918695417 -10.3743161735385 3.2452744609063e-25 2.46640859028879e-24 +TR2779|c0_g1_i1 wt_37 wt_ph8 191.51955185349 1058.15934185376 624.839446853626 -2.46872482043468 0.248047686960726 -9.95262181511715 2.45625242439164e-23 1.55562653544804e-22 +TR1891|c0_g1_i1 wt_37 wt_ph8 131.416087212132 376.595292171713 254.005689691923 -1.51763504949468 0.163833329626194 -9.26328637132227 1.98234808918918e-20 1.07613181984555e-19 +TR1492|c0_g1_i2 wt_37 wt_ph8 2006.11782336441 890.823502721036 1448.47066304272 1.17138763330801 0.127405972315828 9.1941344037173 3.78025797563516e-20 1.7956225384267e-19 +TR2487|c0_g1_i1 wt_37 wt_ph8 418.818667162757 965.862817209246 692.340742186001 -1.2068861494209 0.138672539999103 -8.70313725722991 3.22833072204724e-18 1.36307297153106e-17 +TR3638|c0_g1_i1 wt_37 wt_ph8 713.131183384274 326.063958913919 519.597571149096 1.12959116050603 0.141514345090043 7.98216717737901 1.43786102301281e-15 5.46387188744868e-15 +TR2122|c0_g2_i2 wt_37 wt_ph8 146.135958637131 360.821667264163 253.478812950647 -1.30611123021679 0.169971549866391 -7.68429323168191 1.53843927144259e-14 5.31460839225623e-14 +TR2107|c1_g1_i1 wt_37 wt_ph8 59.5986596731862 1.89840873462066 30.7485342039034 4.94663101068376 0.648801734442532 7.62425676148051 2.45444399374e-14 7.77240598017667e-14 +TR1479|c0_g1_i1 wt_37 wt_ph8 158.005105094407 334.827472148091 246.416288621249 -1.08064044509537 0.165852688009601 -6.51566434083244 7.23686413447896e-11 2.11539105469385e-10 +TR24|c0_g1_i1 wt_37 wt_ph8 85.6614643869141 199.923709280262 142.792586833588 -1.2309601921531 0.197065470330034 -6.24645296860764 4.19878369504523e-10 1.1396698600837e-09 +TR4163|c0_g1_i1 wt_37 wt_ph8 424.593720981574 227.471218917767 326.03246994967 0.902378343080325 0.156120482680009 5.7800125107855 7.46950706225728e-09 1.89227512243851e-08 +TR1449|c0_g1_i1 wt_37 wt_ph8 220.782434528097 117.26089394399 169.021664236043 0.916182468982546 0.175267159439456 5.22734819182728 1.71958482582447e-07 4.08401396133312e-07 +TR2278|c0_g1_i1 wt_37 wt_ph8 594.657329919233 348.341653317169 471.499491618201 0.773725482804612 0.158144801146882 4.8925129197639 9.95565784679224e-07 2.22538234222415e-06 +TR5055|c0_g2_i1 wt_37 wt_ph8 28.6665933385886 6.05959103586122 17.3630921872249 2.22056293047174 0.515653625436262 4.30630722045843 1.66002467176799e-05 3.50449652928799e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 16.3791628279609 1.58772512712498 8.98344397754296 3.35782864860774 0.805715621214412 4.16751091848842 3.0794376698456e-05 6.15887533969119e-05 +TR1894|c2_g1_i1 wt_37 wt_ph8 16.2826445742552 1.67571344127509 8.97917900776516 3.31835899440704 0.806156235895962 4.1162728099709 3.85048512190321e-05 7.31592173161609e-05 +TR2672|c0_g1_i1 wt_37 wt_ph8 22.3129914439134 7.89947501226409 15.1062332280887 1.4879160019133 0.490304786216721 3.03467566244728 0.00240794483755522 0.00435723351557611 +TR4084|c0_g1_i1 wt_37 wt_ph8 113.2594381118 173.837287636503 143.548362874151 -0.610546095515353 0.203809508378262 -2.99567032163291 0.0027384232210324 0.0047300037454196 +TR4859|c0_g1_i1 wt_37 wt_ph8 8.91205730249659 1.28188505334354 5.09697117792006 2.79846628921536 0.94330374949058 2.96666507551426 0.00301048704228199 0.00497384815681373 +TR1678|c0_g1_i1 wt_37 wt_ph8 0.738899982352077 7.85275634721875 4.29582816478541 -3.47431884008145 1.21198503063676 -2.8666351087324 0.00414861034620891 0.00656863304816411 +TR3807|c0_g1_i1 wt_37 wt_ph8 4.23896204531587 0.352255997713617 2.29560902151474 3.60257127355045 1.494771199452 2.41011552461755 0.0159474699414716 0.0242401543110368 +TR1859|c3_g1_i1 wt_37 wt_ph8 0.361569353912422 2.25550826604853 1.30853880998047 -2.58650633406891 1.68391965639604 -1.53600340980911 0.124537544060973 0.181135380859874 +TR3249|c0_g1_i1 wt_37 wt_ph8 1.36481976577862 4.37661229401476 2.87071602989669 -1.67837058189371 1.10474169040967 -1.51924254915312 0.128701454821489 0.181135380859874 +TR2090|c0_g1_i1 wt_37 wt_ph8 0 5.87877087384675 2.93938543692337 -4.93100736412615 3.57047444665656 -1.38105101655149 0.167263275059569 0.227000159009415 +TR1982|c2_g1_i1 wt_37 wt_ph8 7.00144976454503 11.520013112092 9.26073143831853 -0.727260398375605 0.567300823658433 -1.28196605406919 0.199854554547713 0.261878381821141 +TR1837|c2_g1_i1 wt_37 wt_ph8 0.377330628439655 1.67813520813222 1.02773291828594 -2.14007669057536 1.85335822648042 -1.15470212935544 0.248212427250958 0.314402407851213 +TR5212|c0_g1_i1 wt_37 wt_ph8 80.2050001877881 94.8352723753388 87.5201362815635 -0.236625075567937 0.216144030335029 -1.09475646956875 0.273623341840839 0.335409257740383 +TR3854|c0_g1_i1 wt_37 wt_ph8 1925.26464813324 2107.16376011081 2016.21420412203 -0.130625245556186 0.130881633584188 -0.998041069468797 0.318259444082749 0.377933089848265 +TR2844|c0_g1_i1 wt_37 wt_ph8 193.030766468894 213.82243412349 203.426600296192 -0.144061748535941 0.171730922251619 -0.838880654963595 0.401536284440309 0.450271927171227 +TR1122|c0_g1_i1 wt_37 wt_ph8 1.69354093201913 0.660517838352177 1.17702938518565 1.39462173786331 1.66721495733336 0.83649785633758 0.402874882205835 0.450271927171227 +TR2011|c5_g1_i1 wt_37 wt_ph8 6.84875389533898 4.81927837273561 5.8340161340373 0.483956961494249 0.73923753588747 0.654670438120068 0.512679962329314 0.556623959100398 +TR2182|c3_g2_i6 wt_37 wt_ph8 2.76248771922916 1.94482465855284 2.353656188891 0.516404389322082 1.10366040723296 0.467901526536394 0.639855011782969 0.675402512437579 +TR3788|c0_g1_i1 wt_37 wt_ph8 23.7579432209456 26.0024682525169 24.8802057367313 -0.125340757750782 0.352879389384873 -0.35519432849074 0.72244401329073 0.741969527163452 +TR939|c0_g1_i1 wt_37 wt_ph8 103.002135647151 102.820214322362 102.911174984756 0.000973457550311695 0.195891269167832 0.00496937691223835 0.996035027203895 0.996035027203895
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -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
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -1,40 +1,40 @@ sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj -TR2779|c0_g1_i1 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.30255444666643 0.142496869452374 -16.1586318037394 9.87286349195067e-59 3.65295949202175e-57 -TR1891|c0_g1_i1 wt_GSNO wt_ph8 128.246229498835 343.028289972482 235.637259735659 -1.41742353970608 0.104322254921725 -13.5869718380762 4.7847024102546e-42 8.85169945897101e-41 -TR4761|c0_g1_i1 wt_GSNO wt_ph8 184.029205648389 351.782300021135 267.905752834762 -0.941259207260894 0.0933372308442124 -10.0844989587481 6.46943903995441e-24 7.97897481594377e-23 -TR24|c0_g1_i1 wt_GSNO wt_ph8 39.3724575919554 183.288101009647 111.330279300801 -2.22846767043702 0.242443002218043 -9.19171784728532 3.8661704482204e-20 3.57620766460387e-19 -TR3638|c0_g1_i1 wt_GSNO wt_ph8 174.266398355818 297.555274221606 235.910836288712 -0.761689698593786 0.0969314803260852 -7.85802193499368 3.90246977317854e-15 2.88782763215212e-14 -TR2122|c0_g2_i2 wt_GSNO wt_ph8 190.673533226329 328.707071692642 259.690302459485 -0.789061688115738 0.103094089827306 -7.65380139091878 1.95123561208803e-14 1.20326196078762e-13 -TR4669|c0_g2_i1 wt_GSNO wt_ph8 165.630009730314 0 82.8150048651569 9.98638581786287 2.4059110197361 4.15077105343582 3.31357095211564e-05 0.000175145893183255 -TR2278|c0_g1_i1 wt_GSNO wt_ph8 426.804298570637 315.99710709695 371.400702833793 0.433055347501052 0.106340324733669 4.07235306630524 4.65405596936774e-05 0.000215250088583258 -TR4084|c0_g1_i1 wt_GSNO wt_ph8 115.544575735664 157.970364768418 136.757470252041 -0.444508945050626 0.160721197310781 -2.76571449496544 0.00567982380522758 0.0233503867548245 -TR3788|c0_g1_i1 wt_GSNO wt_ph8 128.115824993653 24.010679388938 76.0632521912957 2.41599826196159 0.930388620648254 2.59676248004649 0.00941069736444863 0.0348195802484599 -TR5075|c0_g1_i1 wt_GSNO wt_ph8 8.81552188359314 126.23137395943 67.5234479215117 -3.83892667969009 1.51640337447055 -2.53159993199728 0.011354345783228 0.0381918903617669 -TR1492|c0_g1_i2 wt_GSNO wt_ph8 1368.89238848897 813.514514376559 1091.20345143276 0.750717599362045 0.314762309207928 2.38503015577424 0.0170777214032423 0.0526563076599971 -TR1678|c0_g1_i1 wt_GSNO wt_ph8 0.695005959508731 7.10082184137838 3.89791390044355 -3.29023865439926 1.5074251817588 -2.18268786684349 0.0290588040465388 0.0827058269016874 -TR1479|c0_g1_i1 wt_GSNO wt_ph8 353.92669362375 305.546165789569 329.736429706659 0.212056310257658 0.102841330599285 2.0619755600394 0.0392100628615421 0.0987833713777749 -TR1859|c3_g1_i1 wt_GSNO wt_ph8 0 2.05957798928713 1.02978899464357 -3.32897459707672 1.62131131542189 -2.05326057087961 0.0400473127207196 0.0987833713777749 -TR2844|c0_g1_i1 wt_GSNO wt_ph8 220.566338218013 194.214843050373 207.390590634193 0.186796872895526 0.101161116569868 1.84652838194517 0.0648155222548659 0.149885895214377 -TR2107|c1_g1_i1 wt_GSNO wt_ph8 7.08292121571621 1.78415791317121 4.43353956444371 1.99039306371489 1.13345482120555 1.75604093473959 0.0790814192380851 0.172118383047597 -TR2672|c0_g1_i1 wt_GSNO wt_ph8 2.07518941673641 7.44710458698621 4.76114700186131 -1.80710364026684 1.37881760417113 -1.31061834052603 0.189986739707575 0.390528298287793 -TR4859|c0_g1_i1 wt_GSNO wt_ph8 3.10763825129944 1.1806627783491 2.14415051482427 1.36600125700608 1.2414304168313 1.10034460126467 0.271182006077654 0.528091274993326 -TR3091|c0_g1_i1 wt_GSNO wt_ph8 312.47018793986 293.531643106953 303.000915523406 0.0884824617062972 0.0884687505769758 1.00015498273946 0.317235511103454 0.572534846407878 -TR4163|c0_g1_i1 wt_GSNO wt_ph8 221.469120691076 207.118822998308 214.293971844692 0.0967338751775769 0.0982736079923787 0.984332183927538 0.32495221012339 0.572534846407878 -TR1894|c2_g1_i1 wt_GSNO wt_ph8 2.85762748931802 1.47338219762144 2.16550484346973 0.974874448083219 1.21963227734233 0.799318340612911 0.424105846774723 0.713268924121126 -TR3249|c0_g1_i1 wt_GSNO wt_ph8 2.06512931203634 4.15451161800812 3.10982046502223 -1.06280923847799 1.42172379433194 -0.747549729923031 0.454731796166148 0.726065302514322 -TR5212|c0_g1_i1 wt_GSNO wt_ph8 102.736339436612 86.4452993262187 94.5908193814151 0.250307109752951 0.347207101059694 0.720915871216346 0.470961277306587 0.726065302514322 -TR1122|c0_g1_i1 wt_GSNO wt_ph8 1.29006258579706 0.5946183773076 0.942340481552333 1.01745920560278 1.75106315862361 0.581052259932493 0.56120523253296 1 -TR2011|c5_g1_i1 wt_GSNO wt_ph8 7.597917075274 4.42090354598533 6.00941031062966 0.776221433822186 1.38068634268934 0.562199689981896 0.573979972628347 0.849490359489954 -TR1837|c2_g1_i1 wt_GSNO wt_ph8 2.16507864525674 1.46465683073113 1.81486773799393 0.574055870722254 1.31330872914193 0.437106567545105 0.662034064585522 0.882648546299865 -TR1982|c2_g1_i1 wt_GSNO wt_ph8 5.5352448786851 10.687042573374 8.11114372602957 -0.948745824078601 2.34310116245329 -0.404910312572778 0.685543437736556 0.882648546299865 -TR2182|c3_g2_i6 wt_GSNO wt_ph8 1.29006258579706 1.76655578876639 1.52830918728173 -0.570835750385155 1.46441538912588 -0.389804528567464 0.69668109483689 0.882648546299865 -TR1449|c0_g1_i1 wt_GSNO wt_ph8 98.9943307118646 106.843279101242 102.918804906553 -0.106933839690288 0.276431863357554 -0.386836156988073 0.69887750768045 0.882648546299865 -TR4277|c0_g1_i1 wt_GSNO wt_ph8 153.969096204861 149.159426886469 151.564261545665 0.0465928591854992 0.127909639606222 0.364263861026723 0.715660983486377 0.882648546299865 -TR3854|c0_g1_i1 wt_GSNO wt_ph8 2260.55060252051 1927.46472630351 2094.00766441201 0.229965172704227 0.793466242289153 0.289823511635197 0.771951259799022 0.910963182508483 -TR127|c1_g1_i1 wt_GSNO wt_ph8 1.20754470361908 1.49113571265046 1.34934020813477 -0.373671738849606 1.38864714646401 -0.269090488394483 0.787860049737066 0.910963182508483 -TR2090|c0_g1_i1 wt_GSNO wt_ph8 9.46045896251181 5.6546754787973 7.55756722065455 0.740040477295998 3.75055668025179 0.197314836272869 0.843581169905129 0.945833432923932 -TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.347502979754365 0.292870809896544 0.320186894825454 0.331202385322154 1.89086385045429 0.175159298350635 0.86095446505486 1 -TR131|c0_g1_i1 wt_GSNO wt_ph8 1275.67603302799 1312.2934796972 1293.9847563626 -0.0408368749216097 0.405274721880973 -0.100763439506112 0.919738250126613 0.956831887096638 -TR5055|c0_g2_i1 wt_GSNO wt_ph8 5.17791343714095 5.60171771495863 5.38981557604979 -0.113901914254779 1.2463123048955 -0.0913911495596841 0.927181793948424 0.956831887096638 -TR939|c0_g1_i1 wt_GSNO wt_ph8 92.2508462008296 94.0990807885678 93.1749634946987 -0.0286723936076206 0.345661698999542 -0.0829492931690373 0.933891858779013 0.956831887096638 -TR2487|c0_g1_i1 wt_GSNO wt_ph8 875.181494043204 882.631049341941 878.906271692572 -0.0122873741271452 0.226999049805604 -0.0541296280212089 0.956831887096638 0.956831887096638 +TR2779|c0_g1_i1 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.30255444666643 0.142496869452394 -16.1586318037371 9.87286349231705e-59 3.65295949215731e-57 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 128.246229498835 343.028289972482 235.637259735659 -1.41742353970608 0.104322254921704 -13.586971838079 4.78470241007372e-42 8.85169945863638e-41 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 184.029205648389 351.782300021135 267.905752834762 -0.941259207260895 0.0933372308442406 -10.0844989587451 6.4694390401545e-24 7.97897481619054e-23 +TR24|c0_g1_i1 wt_GSNO wt_ph8 39.3724575919554 183.288101009647 111.330279300801 -2.22846767043702 0.242443002218073 -9.19171784728418 3.86617044826114e-20 3.57620766464156e-19 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 174.266398355818 297.555274221606 235.910836288712 -0.761689698593791 0.096931480326081 -7.85802193499407 3.90246977316646e-15 2.88782763214318e-14 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 190.673533226329 328.707071692642 259.690302459485 -0.789061688115737 0.103094089827314 -7.65380139091815 1.95123561209759e-14 1.20326196079352e-13 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 165.630009730314 0 82.8150048651569 9.98638581786287 2.40591101973569 4.15077105343653 3.31357095210528e-05 0.000175145893182708 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 426.804298570637 315.99710709695 371.400702833793 0.433055347501054 0.106340324733697 4.07235306630417 4.65405596938926e-05 0.000215250088584253 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 115.544575735664 157.970364768418 136.757470252041 -0.444508945050625 0.160721197310796 -2.76571449496517 0.00567982380523222 0.0233503867548436 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 128.115824993653 24.010679388938 76.0632521912957 2.41599826196159 0.930388620648679 2.59676248004531 0.00941069736448111 0.0348195802485801 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 8.81552188359314 126.23137395943 67.5234479215117 -3.83892667969009 1.51640337447128 -2.53159993199606 0.0113543457832674 0.0381918903618995 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 1368.89238848897 813.514514376559 1091.20345143276 0.750717599362044 0.314762309207961 2.38503015577399 0.0170777214032538 0.0526563076600326 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 0.695005959508731 7.10082184137838 3.89791390044355 -3.29023865439928 1.50742518175894 -2.18268786684328 0.0290588040465541 0.0827058269017309 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 353.92669362375 305.546165789569 329.736429706659 0.212056310257659 0.102841330599274 2.06197556003964 0.0392100628615187 0.0987833713777822 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 0 2.05957798928713 1.02978899464357 -3.32897459707671 1.62131131542191 -2.05326057087958 0.0400473127207225 0.0987833713777822 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 220.566338218013 194.214843050373 207.390590634193 0.186796872895529 0.101161116569857 1.8465283819454 0.0648155222548327 0.149885895214301 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 7.08292121571621 1.78415791317121 4.43353956444371 1.99039306371489 1.13345482120575 1.75604093473928 0.0790814192381375 0.172118383047711 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 2.07518941673641 7.44710458698621 4.76114700186131 -1.80710364026684 1.3788176041713 -1.31061834052587 0.189986739707629 0.390528298287903 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 3.10763825129944 1.1806627783491 2.14415051482427 1.36600125700608 1.24143041683139 1.1003446012646 0.271182006077686 0.528091274993389 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 312.47018793986 293.531643106953 303.000915523406 0.0884824617062953 0.0884687505769775 1.00015498273942 0.317235511103473 0.572534846408031 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 221.469120691076 207.118822998308 214.293971844692 0.0967338751775785 0.098273607992398 0.984332183927362 0.324952210123477 0.572534846408031 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 2.85762748931802 1.47338219762144 2.16550484346973 0.974874448083218 1.21963227734242 0.799318340612854 0.424105846774756 0.713268924121181 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 2.06512931203634 4.15451161800812 3.10982046502223 -1.06280923847798 1.42172379433197 -0.747549729923012 0.454731796166159 0.726065302514524 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 102.736339436612 86.4452993262187 94.5908193814151 0.250307109752951 0.347207101059796 0.720915871216134 0.470961277306718 0.726065302514524 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 1.29006258579706 0.5946183773076 0.942340481552333 1.01745920560277 1.75106315862354 0.581052259932512 0.561205232532948 1 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 7.597917075274 4.42090354598533 6.00941031062966 0.776221433822191 1.38068634268979 0.562199689981717 0.573979972628469 0.849490359490134 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 2.16507864525674 1.46465683073113 1.81486773799393 0.574055870722253 1.31330872914198 0.437106567545087 0.662034064585536 0.882648546299866 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 5.5352448786851 10.687042573374 8.11114372602957 -0.9487458240786 2.34310116245464 -0.404910312572544 0.685543437736728 0.882648546299866 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 1.29006258579706 1.76655578876639 1.52830918728173 -0.570835750385155 1.46441538912588 -0.389804528567465 0.69668109483689 0.882648546299866 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 98.9943307118646 106.843279101242 102.918804906553 -0.106933839690289 0.276431863357607 -0.386836156987999 0.698877507680504 0.882648546299866 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 153.969096204861 149.159426886469 151.564261545665 0.0465928591855008 0.127909639606227 0.364263861026722 0.715660983486378 0.882648546299866 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 2260.55060252051 1927.46472630351 2094.00766441201 0.229965172704227 0.793466242289089 0.289823511635221 0.771951259799004 0.910963182508494 +TR127|c1_g1_i1 wt_GSNO wt_ph8 1.20754470361908 1.49113571265046 1.34934020813477 -0.373671738849602 1.38864714646406 -0.269090488394471 0.787860049737076 0.910963182508494 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 9.46045896251181 5.6546754787973 7.55756722065455 0.740040477295999 3.75055668025179 0.19731483627287 0.843581169905129 0.945833432923932 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.347502979754365 0.292870809896544 0.320186894825454 0.331202385322155 1.89086385045428 0.175159298350637 0.860954465054859 1 +TR131|c0_g1_i1 wt_GSNO wt_ph8 1275.67603302799 1312.2934796972 1293.9847563626 -0.0408368749216137 0.405274721880999 -0.100763439506115 0.91973825012661 0.956831887096637 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 5.17791343714095 5.60171771495863 5.38981557604979 -0.113901914254778 1.2463123048958 -0.0913911495596612 0.927181793948442 0.956831887096637 +TR939|c0_g1_i1 wt_GSNO wt_ph8 92.2508462008296 94.0990807885678 93.1749634946987 -0.0286723936076184 0.345661698999674 -0.0829492931689995 0.933891858779043 0.956831887096637 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 875.181494043204 882.631049341941 878.906271692572 -0.0122873741271473 0.22699904980564 -0.0541296280212096 0.956831887096637 0.956831887096637
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -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
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results Tue Apr 11 19:51:53 2023 +0000 @@ -1,40 +1,40 @@ sampleA sampleB logFC logCPM PValue FDR -TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23795519272237 15.9076254017254 2.92187316761645e-09 1.13953053537042e-07 -TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807554446371668 16.8426446227048 5.58321346448906e-08 1.08872662557537e-06 -TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16839334936064 13.5222768601527 3.73856822091501e-07 4.86013868718952e-06 -TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47096654484901 13.0144557887788 1.245732049043e-06 9.71670998253539e-06 -TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.68481140303272 12.7944067233298 3.44359702134355e-06 2.23833806387331e-05 -TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.290746293924475 17.7782076349597 5.25322144866517e-07 5.12189091244854e-06 -TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.35768165107067 14.6117632515968 5.28666359293828e-06 2.79053243123467e-05 -TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.878920056028248 14.8002262876656 5.72416908971214e-06 2.79053243123467e-05 -TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.730166040402744 14.7551588447381 0.000213340170514583 0.000924474072229861 -TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.708321413581678 14.6195575978943 0.000258928735946659 0.00100982207019197 -TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.90861736829884 8.90712643491077 0.00457979737107378 0.0148843414559898 -TR1678|c0_g1_i1 wt_GSNO wt_ph8 -2.86408187112217 8.67828416118206 0.00614682516189 0.01844047548567 -TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.503051556783977 15.2850549214884 0.00155857674629228 0.00552586300958173 -TR1859|c3_g1_i1 wt_GSNO wt_ph8 -1.96144637998691 6.77065030795652 0.0428269385052548 0.0982500353944082 -TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.69730734417424 8.97832173338033 0.0866262290356731 0.160877282494822 -TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.277933522953326 15.1098597149167 0.0157877120065803 0.0439800548754737 -TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.859948395691952 9.74982883974683 0.0845253825418736 0.160877282494822 -TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.04376243585308 7.84838377560073 0.178339170085147 0.289801151388364 -TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.835627288758852 9.33803398810951 0.117576176969539 0.20843049553691 -TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.383433512314591 13.8345091917852 0.0320674039619619 0.083375250301101 -TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.899367664455804 7.86698528437277 0.236693956821629 0.369242572641742 -TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.317453614519532 13.3093804544918 0.0408068910563242 0.0982500353944082 -TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.988859576038597 7.34392475064937 0.332144974966109 0.462630500845651 -TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.18548803762213 8.36747688877935 0.296376188714782 0.444564283072173 -TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.83411458992077 7.6102620160458 0.393260306376011 0.528867308574635 -TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.40219136988549 5.09566487188118 0.681998347783062 0.765740423023185 -TR4669|c0_g2_i1 wt_GSNO wt_ph8 6.05037553674292 13.1239272719772 0.480074268471172 0.603964402270185 +TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23795519272236 15.9076254017254 2.92187316761747e-09 1.13953053537081e-07 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807554446371668 16.8426446227048 5.58321346449028e-08 1.0887266255756e-06 +TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16839334936065 13.5222768601527 3.73856822091552e-07 4.86013868719017e-06 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47096654484901 13.0144557887788 1.24573204904324e-06 9.71670998253725e-06 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.68481140303272 12.7944067233298 3.44359702134402e-06 2.23833806387361e-05 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.290746293924475 17.7782076349597 5.253221448666e-07 5.12189091244935e-06 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.35768165107067 14.6117632515968 5.28666359293914e-06 2.79053243123478e-05 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.87892005602825 14.8002262876656 5.72416908971236e-06 2.79053243123478e-05 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.73016604040274 14.7551588447381 0.000213340170514584 0.000924474072229863 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.708321413581678 14.6195575978943 0.000258928735946679 0.00100982207019205 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.90861736829884 8.90712643491077 0.00457979737107358 0.0148843414559891 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 -2.86408187112217 8.67828416118206 0.00614682516188998 0.01844047548567 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.503051556783975 15.2850549214884 0.00155857674629243 0.00552586300958226 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 -1.96144637998691 6.77065030795652 0.0428269385052536 0.0982500353944054 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.69730734417424 8.97832173338033 0.0866262290356742 0.160877282494824 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.277933522953328 15.1098597149167 0.0157877120065796 0.0439800548754716 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.859948395691952 9.74982883974683 0.0845253825418728 0.160877282494824 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.04376243585308 7.84838377560073 0.178339170085145 0.28980115138836 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.835627288758852 9.33803398810951 0.117576176969538 0.208430495536908 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.383433512314591 13.8345091917852 0.0320674039619627 0.0833752503011029 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.899367664455804 7.86698528437277 0.236693956821627 0.369242572641738 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.317453614519528 13.3093804544918 0.0408068910563263 0.0982500353944054 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.988859576038597 7.34392475064937 0.332144974966108 0.46263050084565 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.18548803762212 8.36747688877935 0.296376188714785 0.444564283072177 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.83411458992077 7.6102620160458 0.39326030637601 0.528867308574635 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.40219136988549 5.09566487188118 0.681998347783058 0.765740423023183 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 6.05037553674292 13.1239272719772 0.480074268471177 0.603964402270191 TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.184244267394782 6.64199260311611 0.869699168726351 0.892585988955992 -TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.354388761220407 7.15556768591471 0.687202943738756 0.765740423023185 -TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.251980888130202 14.4425124782726 0.0594765231313145 0.128865800117848 -TR2090|c0_g1_i1 wt_GSNO wt_ph8 -0.862128177746631 9.64998833298881 0.646749723219784 0.764340581987017 -TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.148831558112849 14.9878570236746 0.0841354210369957 0.160877282494822 +TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.354388761220407 7.15556768591471 0.687202943738754 0.765740423023183 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.251980888130197 14.4425124782726 0.0594765231313182 0.128865800117856 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 -0.862128177746631 9.64998833298881 0.646749723219787 0.764340581987021 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.148831558112851 14.9878570236746 0.0841354210369898 0.160877282494824 TR5055|c0_g2_i1 wt_GSNO wt_ph8 0.0583511298028353 9.18288041060754 0.918331019801174 0.918331019801174 -TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.161834057105857 14.4879250602579 0.126768900432688 0.214955961603254 -TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.103273026252208 13.9874746529507 0.30829078508145 0.445308911784317 -TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0333503331526365 13.2856573711711 0.715260879184748 0.774865952450143 -TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.049884213852527 13.4293306544833 0.75234222467997 0.793009371959969 -TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0480185034754555 16.5239765307922 0.407818984620182 0.530164680006236 -TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0203187870937255 17.0810493411762 0.539920494505425 0.658028102678487 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.161834057105863 14.4879250602579 0.126768900432678 0.214955961603237 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.103273026252208 13.9874746529507 0.308290785081446 0.445308911784311 +TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0333503331526316 13.2856573711711 0.71526087918478 0.774865952450178 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.049884213852527 13.4293306544833 0.752342224679971 0.793009371959969 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0480185034754555 16.5239765307922 0.407818984620183 0.530164680006237 +TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0203187870937285 17.0810493411762 0.539920494505375 0.658028102678426
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
Binary file test-data/count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf has changed
--- a/test-data/filtered/Trinity_filtered_exp.fasta Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_exp.fasta Tue Apr 11 19:51:53 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
--- a/test-data/filtered/Trinity_filtered_hi_iso.fasta Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta Tue Apr 11 19:51:53 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
--- a/test-data/filtered/Trinity_filtered_pct_iso.fasta Sun Dec 19 16:19:00 2021 +0000 +++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta Tue Apr 11 19:51:53 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