# HG changeset patch
# User iuc
# Date 1681242765 0
# Node ID a009c96c5c18fe1d850659b3f8fef47aee30f6e2
# Parent  bcc5f03f19000d0cc20230c9d69b3ddd0a81deee
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 1d443e73d2eb888660bbbc7af198f5bcca9c1a70

diff -r bcc5f03f1900 -r a009c96c5c18 abundance_estimates_to_matrix.xml
--- a/abundance_estimates_to_matrix.xml	Sun Dec 19 16:17:05 2021 +0000
+++ b/abundance_estimates_to_matrix.xml	Tue Apr 11 19:52:45 2023 +0000
@@ -1,13 +1,10 @@
-<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@">
+<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
     <description>for a de novo assembly of RNA-Seq data by Trinity</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="0.44.0">kallisto</requirement>
-    </expand>
+    <expand macro="requirements"/>
     <command detect_errors="aggressive"><![CDATA[
         #import re
         #for $entry in $samples:
@@ -49,9 +46,9 @@
         #end if
     ]]></command>
     <inputs>
-        <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" />
-        <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" optional="true" help="Only needed for gene level estimates" />
-        <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method">
+        <param name="samples" type="data" format="tabular" multiple="true" label="Abundance estimates" help="output(s) from 'Align reads and estimate abundance' tool" />
+        <param argument="--gene_trans_map" type="data" format="tabular" optional="true"  label="Gene to transcript correspondence ('gene(tab)transcript' lines)" help="Only needed for gene level estimates" />
+        <param type="select" argument="--est_method" label="Abundance estimation method">
             <option value="RSEM">RSEM</option>
             <option value="eXpress">eXpress</option>
             <option value="salmon">Salmon</option>
@@ -59,7 +56,7 @@
         </param>
 
         <section name="additional_params" title="Additional Options" expanded="False">
-            <param type="select" name="cross_sample_norm" argument="--cross_sample_norm" label="Cross sample normalization">
+            <param type="select" argument="--cross_sample_norm" label="Cross sample normalization">
                 <option value="TMM">TMM</option>
                 <option value="UpperQuartile">UpperQuartile</option>
                 <option value="none">None</option>
@@ -68,26 +65,26 @@
     </inputs>
     <outputs>
         <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/>
-        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of isoform TPM expression values (not cross-sample normalized)"/>
+        <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: Matrix of isoform TPM expression values (not cross-sample normalized)"/>
 
         <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)">
             <filter>gene_trans_map</filter>
         </data>
-        <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: matrix of gene TPM expression values (not cross-sample normalized)">
+        <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: Matrix of gene TPM expression values (not cross-sample normalized)">
             <filter>gene_trans_map</filter>
         </data>
 
-        <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
+        <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values">
             <filter>additional_params['cross_sample_norm'] == "TMM"</filter>
         </data>
-        <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
+        <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values">
             <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter>
         </data>
 
-        <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values">
+        <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: Matrix of TMM-normalized expression values (gene)">
             <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter>
         </data>
-        <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values">
+        <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: Matrix of UpperQuartile-normalized expression values (gene)">
             <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter>
         </data>
     </outputs>
diff -r bcc5f03f1900 -r a009c96c5c18 macros.xml
--- a/macros.xml	Sun Dec 19 16:17:05 2021 +0000
+++ b/macros.xml	Tue Apr 11 19:52:45 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>
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf
Binary file test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix
--- a/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_1_log2_medianCentered_fpkm.matrix	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix
--- a/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/define_clusters_by_cutting_tree/subcluster_2_log2_medianCentered_fpkm.matrix	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results
--- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf
Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf
Binary file test-data/count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf
Binary file test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/qcheck/wt_37.rep_compare.pdf
Binary file test-data/count/qcheck/wt_37.rep_compare.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/qcheck/wt_GSNO.rep_compare.pdf
Binary file test-data/count/qcheck/wt_GSNO.rep_compare.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/count/qcheck/wt_ph8.rep_compare.pdf
Binary file test-data/count/qcheck/wt_ph8.rep_compare.pdf has changed
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/filtered/Trinity_filtered_exp.fasta
--- a/test-data/filtered/Trinity_filtered_exp.fasta	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/filtered/Trinity_filtered_exp.fasta	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/filtered/Trinity_filtered_hi_iso.fasta
--- a/test-data/filtered/Trinity_filtered_hi_iso.fasta	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/filtered/Trinity_filtered_hi_iso.fasta	Tue Apr 11 19:52:45 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
diff -r bcc5f03f1900 -r a009c96c5c18 test-data/filtered/Trinity_filtered_pct_iso.fasta
--- a/test-data/filtered/Trinity_filtered_pct_iso.fasta	Sun Dec 19 16:17:05 2021 +0000
+++ b/test-data/filtered/Trinity_filtered_pct_iso.fasta	Tue Apr 11 19:52:45 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