| Previous changeset 1:a01453baaf5e (2024-01-23) Next changeset 3:04c26050d2d0 (2024-03-04) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 30fe10acdf65c6917856a0eae21dc91abd2f609f |
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modified:
dimet_pca_analysis.xml macros.xml |
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added:
test-data/CorrectedIsotopologues_5.csv test-data/FracContribution_C_5.csv test-data/abundance--cell-Control-L-Cycloserine-pearson.tsv test-data/abundance--med-Control-L-Cycloserine-pearson.tsv test-data/example5_metadata.csv test-data/isotop_prop--cell--MDV-Control-L-Cycloserine--T0-pearson.tsv test-data/isotop_prop--cell--MDV-Control-L-Cycloserine--T2h-pearson.tsv test-data/isotop_prop--cell--MDV-T2h-T0--Control-pearson.tsv test-data/isotop_prop--cell--MDV-T2h-T0--L-Cycloserine-pearson.tsv test-data/isotop_prop--med--MDV-Control-L-Cycloserine--T0-pearson.tsv test-data/isotop_prop--med--MDV-Control-L-Cycloserine--T2h-pearson.tsv test-data/isotop_prop--med--MDV-T2h-T0--Control-pearson.tsv test-data/isotop_prop--med--MDV-T2h-T0--L-Cycloserine-pearson.tsv test-data/rawAbundances_5.csv |
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| diff -r a01453baaf5e -r c0103ea608fc dimet_pca_analysis.xml --- a/dimet_pca_analysis.xml Tue Jan 23 14:57:12 2024 +0000 +++ b/dimet_pca_analysis.xml Thu Feb 15 12:51:04 2024 +0000 |
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| @@ -205,9 +205,9 @@ **Available data for testing** -You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent +You can test our tool with the data from our manuscript https://zenodo.org/record/10579862 (the pertinent files for you are located in the subfolders inside the data folder). -You can also use the minimal data examples from https://zenodo.org/record/8380706 +You can also use the minimal data examples from https://zenodo.org/record/10579891 ]]> </help> |
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| diff -r a01453baaf5e -r c0103ea608fc macros.xml --- a/macros.xml Tue Jan 23 14:57:12 2024 +0000 +++ b/macros.xml Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| b'@@ -1,42 +1,46 @@\n <macros>\n- <token name="@TOOL_VERSION@">0.1.4</token>\n+ <token name="@TOOL_VERSION@">0.2.1</token>\n <token name="@VERSION_SUFFIX@">1</token>\n <token name="@EXECUTABLE@">pca</token>\n- <xml name="factor_repeat">\n- <repeat name="rep_factorName" title="Factor" min="1">\n- <param name="factorName" type="text" value="FactorName" label="Specify a factor name, e.g. effects_drug_x or cancer_markers"\n- help="Only letters, numbers and underscores will be retained in this field">\n- <sanitizer>\n- <valid initial="string.letters,string.digits"><add value="_" /></valid>\n- </sanitizer>\n- </param>\n- <repeat name="rep_factorLevel" title="Factor level" min="2" default="2">\n- <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be \'tumor\', \'normal\', \'treated\' or \'control\'"\n- help="Only letters, numbers and underscores will be retained in this field">\n- <sanitizer>\n- <valid initial="string.letters,string.digits"><add value="_" /></valid>\n- </sanitizer>\n- </param>\n- <yield/>\n- </repeat>\n- </repeat>\n- </xml>\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>\n </requirements>\n </xml>\n+ <xml name="statistical_test_for_multigroup">\n+ <param name="stat_test" type="select" value="KW" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">\n+ <option value="KW">Kruskal-Wallis</option>\n+ </param>\n+ </xml>\n <xml name="statistical_test">\n- <param name="stat_test" type="select" value="Tt" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">\n- <option value="Tt">t-test</option>\n- <option value="MW">Mann Whitney</option>\n- <option value="KW">Kruskall Wallis</option>\n- <option value="ranksum">Wilcoxon\'s rank sum test</option>\n- <option value="Wcox">Wilcoxon signed-rank test</option>\n- <option value="BrMu">Brunner-Munzel test</option>\n- <option value="prm-scipy">permutations test</option>\n- <option value="disfit">distribution fitting (of the z-score of the ratios), disfit needs several hundreds of metabolites to be trustful.</option>\n- </param>\n+ <conditional name="statistics">\n+ <param name="statistical_test_type" type="select" label="Choose which type of statistical test to perform" help="Choose which type of statistical test to perform">\n+ <option value="parametric">parametric</option>\n+ <option value="non-parametric-rank" selected="true">non-parametric (rank based)</option>\n+ <option value="non-parametric-distribution">non-parametric (distribution based)</option>\n+ </param>\n+ <when value="parametric">\n+ <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">\n+ <option value="Tt" selected="true">t-test</option>\n+ </param>\n+ </when>\n+ <when value="non-parametric-rank">\n+ <param name="stat_test" type="select" display="radio" label="Select statistical to apply" help="Please enter at max 1 statistical test by file">\n+ <option value="MW">Mann Whitney</option>\n+ <option value="KW">Kruskal-Wallis</option>\n+ <option value="ranksum" selected="true">Wilcoxon\'s rank sum test</option>\n+ <option value="Wcox">Wilcoxon signed-rank test</option>\n+ <optio'..b'+ #set $cpt = str($i+1)\n+ $conditions.append(re.sub(\'"\', \'\', str($s.condition)))\n+ #end for\n+\n+ ]]></token>\n+ <token name="@INIT_BIVAR_COMPARISONS@"><![CDATA[\n+ #import re\n+ #set $conditions = list()\n+ #for $i, $s in enumerate($plot_factor_list)\n+ #set $cpt = str($i+1)\n+ $conditions.append(re.sub(\'"\', \'\', str($s.condition)))\n #end for\n+ ]]></token>\n+ <token name="@INIT_COMPARISONS_METABOLOGRAM@"><![CDATA[\n+ #import re\n+ #set $conditions = list()\n+ #set $timepoints = list()\n+ #set $comparisons = list()\n+ #for $i, $s in enumerate($deg_list)\n+ #set $cpt = str($i+1)\n+ #set $comparisons_bis = list()\n+ #for $j, $t in enumerate($s.factor_list)\n+ #set $sub_comparisons = list()\n+ #if str($t.condition) not in $conditions:\n+ $conditions.append(re.sub(\'"\', \'\', str($t.condition)))\n+ #end if\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($t.condition)))\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($s.timepoint)))\n+ $comparisons_bis.append($sub_comparisons)\n+ #end for\n+ $timepoints.append(re.sub(\'"\', \'\', str($s.timepoint)))\n+ $comparisons.append($comparisons_bis)\n+ #end for\n+\n+\n \n ]]></token>\n <token name="@INIT_COMPARISONS@"><![CDATA[\n@@ -753,6 +1014,75 @@\n #end if\n #end if\n ]]></token>\n+ <token name="@INIT_DIFF_ANALYSIS_COMPARISONS@"><![CDATA[\n+ #import re\n+ #set $conditions = list()\n+ #for $i, $s in enumerate($factor_list)\n+ #set $cpt = str($i+1)\n+ $conditions.append(re.sub(\'"\', \'\', str($s.condition)))\n+ #end for\n+\n+ #set $timepoints = list()\n+ #for $tp in $timepoint:\n+ $timepoints.append(re.sub(\'"\', \'\', str($tp)))\n+ #end for\n+\n+ #set $comparisons = list()\n+ #if len($conditions) > 1:\n+ #if len($timepoints) > 0:\n+ #for $tp in $timepoint:\n+ #set $ctrl_found=False\n+ #set $ctrl=""\n+ #set $comparisons_bis = list()\n+\n+ #for $co in $conditions:\n+ #set $sub_comparisons = list()\n+ #if str($co) in ["\'Control\'", "\'control\'", "\'ctrl\'"]:\n+ #set $ctrl_found=True\n+ #set $ctrl=str($co)\n+ #else:\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($co)))\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($tp)))\n+\n+ #end if\n+ $comparisons_bis.append($sub_comparisons)\n+ #end for\n+\n+ #if $ctrl_found:\n+ $sub_comparisons.append(str($ctrl))\n+ $sub_comparisons.append(str($tp))\n+ $comparisons_bis.append($sub_comparisons)\n+ #end if\n+\n+ $comparisons.append($comparisons_bis)\n+ #end for\n+ #else\n+ #for $co in $conditions:\n+ $comparisons.append(re.sub(\'"\', \'\', str($co)))\n+ #end for\n+ #end if\n+\n+ #else\n+ #if len($conditions) > 0:\n+ #if len($timepoints) > 1:\n+ #for $co in $conditions:\n+ #set $comparisons_bis = list()\n+ #for $tp in $timepoint:\n+ #set $sub_comparisons = list()\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($co)))\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($tp)))\n+ $comparisons_bis.append($sub_comparisons)\n+ #end for\n+ $comparisons.append($comparisons_bis)\n+ #end for\n+ #end if\n+ #else\n+ #for $tp in $timepoint:\n+ $comparisons.append(re.sub(\'"\', \'\', str($tp)))\n+ #end for\n+ #end if\n+ #end if\n+ ]]></token>\n <token name="@INIT_TRANSCRIPTS@"><![CDATA[\n #import re\n #import os\n' |
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| diff -r a01453baaf5e -r c0103ea608fc test-data/CorrectedIsotopologues_5.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CorrectedIsotopologues_5.csv Thu Feb 15 12:51:04 2024 +0000 |
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| @@ -0,0 +1,52 @@ +ID MCF001089_TD01 MCF001089_TD02 MCF001089_TD07 MCF001089_TD08 MCF001089_TD19 MCF001089_TD20 MCF001089_TD25 MCF001089_TD26 MCF001089_TD37 MCF001089_TD38 MCF001089_TD43 MCF001089_TD44 MCF001089_TD55 MCF001089_TD56 MCF001089_TD61 MCF001089_TD62 +Fructose_1,6-bisphosphate_m+0 1 0 1 0.5 0.9 +Fructose_1,6-bisphosphate_m+1 0 0 0 0 0.001 0 +Fructose_1,6-bisphosphate_m+2 0 0 0 0 0 +Fructose_1,6-bisphosphate_m+3 0 0 0 0 0 +Fructose_1,6-bisphosphate_m+4 0 1 0 0.5 0.001 0.1 +Fructose_1,6-bisphosphate_m+5 0 0 0 0 0 +Fructose_1,6-bisphosphate_m+6 0 0 0 0 0 +Fumaric_acid_m+0 1 1 0.9979 1 1 +Fumaric_acid_m+1 0 0 0 0 0 +Fumaric_acid_m+2 0 0 0.0043 0 0.0009 +Fumaric_acid_m+3 0.0004 0.0006 0 0 0.0013 +Fumaric_acid_m+4 0.0003 0.0004 0.0004 0.0003 0.0005 0.0003 +Glycine_m+0 0.5 0.5 0.25 0.3 0.001 0.001 0.2 0 0.7 0.6 0.25 0.3 +Glycine_m+1 0.2 0.2 0.55 0.6 0.2 0.2 0.3 0.5 0.3 0.4 0.55 0.6 +Glycine_m+2 0.001 0.001 0 0.1 0.5 0.5 0.5 0.5 0 0 0 0.1 +L-Alanine_m+0 0.7 0.77 1 1 0 0 0.7 0.77 +L-Alanine_m+1 0.3 0.23 0 0 0.01 0.01 0.3 0.23 +L-Alanine_m+2 0.01 0.01 0 0.0002 0.211 0.211 0 0 +L-Alanine_m+3 0 0 0.0055 0.0069 0.699 0.699 0 0 0 0 0 0.0037 0 0 0 0 +L-Arginine_m+0 0.07 0.07 0 0 0.0001 0.0001 0 0 1 0 0 0 0 0 0 0 +L-Arginine_m+1 0.06 0.06 0 0 0.02 0.02 0 1 0 0 0 0 0 0 0 1 +L-Arginine_m+2 0.05 0.05 0 0 0.03 0.03 0 0 0 0 0 0 1 0 0 0 +L-Arginine_m+3 0.04 0.04 1 1 0.04 0.04 1 0 0 1 1 1 0 1 1 0 +L-Arginine_m+4 0.03 0.03 0 0 0.05 0.05 0 0 0 0 0 0 0 0 0 0 +L-Arginine_m+5 0.02 0.02 0 0 0.06 0.06 0 0 0 0 0 0 0 0 0 0 +L-Arginine_m+6 0.0001 0.0001 0 0 0.07 0.07 0 0 0 0 0 0 0 0 0 0 +L-Aspartic_acid_m+0 0.9863 0.9866 0.745 0.7303 0 0.001 0.7523 0.7437 +L-Aspartic_acid_m+1 0.0004 0 0.0716 0.0701 0.0014 0.0021 0.0635 0.063 +L-Aspartic_acid_m+2 0.0117 0.0131 0.1214 0.1303 0.0159 0.0141 0.1137 0.1193 +L-Aspartic_acid_m+3 0.0016 0.0008 0.055 0.0573 0.2 0.18 0.0589 0.0596 +L-Aspartic_acid_m+4 0 0 0.007 0.012 0 0 0.0117 0.0143 +L-Glutamic_acid_m+0 0.5 0.5 0.5577 0.5714 0.001 0.001 0.5577 0.5556 +L-Glutamic_acid_m+1 0.23 0.23 0.0737 0.0687 0.04 0.04 0.0715 0.0688 +L-Glutamic_acid_m+2 0.13 0.13 0.2485 0.2455 0.1 0.1 0.2477 0.2507 +L-Glutamic_acid_m+3 0.1 0.1 0.0619 0.057 0.13 0.13 0.0628 0.0625 +L-Glutamic_acid_m+4 0.04 0.04 0.0487 0.0477 0.23 0.23 0.0508 0.0506 +L-Glutamic_acid_m+5 0.001 0.001 0.0094 0.0096 0.5 0.5 0.0095 0.0118 +L-Glutamine_m+0 1 0.4 0.4 0.2 0.6673 +L-Glutamine_m+1 0 0.0347 0.34 0 0.0526 +L-Glutamine_m+2 0.01 0.1482 0.009 0.0104 0.1919 +L-Glutamine_m+3 0 0.2371 0 0 0.043 +L-Glutamine_m+4 0 0.0263 0 0.36 0.0374 +L-Glutamine_m+5 0 0.0053 0 0.04 0.0078 +L-Lactic_acid_m+0 0 0 0.9878 0.9883 0.9878 0.9883 0 0 0.0155 0.0168 0.0173 0.0191 0.0147 0.0135 0.0229 0.0165 +L-Lactic_acid_m+1 0 0 0.0122 0.0117 0.0122 0.0117 0 0 0.0002 0.0002 0.0002 0.0002 0.0002 0.0002 0.0001 0.0002 +L-Lactic_acid_m+2 0.0115 0.0121 0.0001 0 0.0001 0 0.0115 0.0121 0.0121 0.012 0.0121 0.012 0.012 0.0121 0.0118 0.0119 +L-Lactic_acid_m+3 0.9885 0.9879 0 0.0001 0 0.0001 0.9885 0.9879 0.9723 0.9709 0.9704 0.9687 0.9731 0.9742 0.9651 0.9713 +Pyruvic_acid_m+0 0.08 0.07 0.3 0.2 0.57 0.6 0.01 0.3 0.1 0.1 0.3 0.2 0.57 0.6 0.01 0.3 +Pyruvic_acid_m+1 0.12 0.13 0.3 0.6 0.23 0.2 0.15 0.2 0.1 0.1 0.3 0.6 0.23 0.2 0.15 0.2 +Pyruvic_acid_m+2 0.2 0.23 0.3 0.15 0.0001 0.0001 0.35 0.2 0.2 0.23 0.3 0.15 0.1 0.1 0.35 0.2 +Pyruvic_acid_m+3 0.6 0.57 0.1 0.15 0.0005 0.0005 0.25 0.3 0.6 0.57 0.1 0.15 0.1 0.1 0.25 0.3 |
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| diff -r a01453baaf5e -r c0103ea608fc test-data/FracContribution_C_5.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FracContribution_C_5.csv Thu Feb 15 12:51:04 2024 +0000 |
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| @@ -0,0 +1,26 @@ +ID MCF001089_TD01 MCF001089_TD02 MCF001089_TD07 MCF001089_TD08 MCF001089_TD19 MCF001089_TD20 MCF001089_TD25 MCF001089_TD26 MCF001089_TD37 MCF001089_TD38 MCF001089_TD43 MCF001089_TD44 MCF001089_TD55 MCF001089_TD56 MCF001089_TD61 MCF001089_TD62 +Fructose_1,6-bisphosphate 0.0 0.0 0.0 0.0 0.0 +Fumaric_acid 0.0 0.0 0.0 0.00189664357263286 0.0 0.0 0.000500041300531799 +Glycine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +Hexose 0.00762749174596484 0.00167577130357252 0.00509338901447358 0.00252875218461319 0.00575687494289638 0.00521882313638746 0.0041732481389427 0.00462441914606014 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +Hexose-phosphate 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +Ile_Leu 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Alanine 0.000300183098510707 0.0 0.0180323570915377 0.0208864367091383 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Arginine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Asparagine 0.0 0.0 0.0 0.0 0.00275043348149139 0.0 0.0 0.0 +L-Aspartic_acid 0.00711429300863751 0.00711565170397871 0.126874713735778 0.137607007753336 0.00887214703655263 0.00814181833419956 0.128546005517517 0.134463940877588 +L-Glutamic_acid 0.0186189922849795 0.0189512529072842 0.199700486213809 0.193976641844404 0.0186857662222136 0.0202828476474173 0.20124661989943 0.203786827442622 +L-Glutamine 0.00160200012909904 0.0 0.114887862236339 0.139366599094848 0.00227741586424723 0.0022177382266197 0.125412764443405 0.150842877169667 +L-Histidine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Lactic_acid 0.996169569495619 0.995975477500888 0.99592721423554 0.996105017845211 0.99599115961227 0.99599772879137 0.996132991391358 0.996246688151202 0.980373866526704 0.979007295796873 0.978534478509106 0.976787596299441 0.981176728749348 0.982344821248399 0.973048888977137 0.979345434097336 +L-Lysine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Malic_acid 3.53420625487163e-05 8.4896366324339e-05 0.00753337452964479 0.0113698929771914 0.0 0.0 0.00614506153792491 0.00843804328368624 +L-Methionine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Phenylalanine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Proline 0.00610056503723104 0.00513475924422191 0.016636816203803 0.0146250924721546 0.00333324651935455 0.00398908903111498 0.0133985852742358 0.0146846667756098 0.000911540747703803 0.00221029683948302 0.00846057868350799 0.0 0.0 0.0 0.0022582830613801 0.0 +L-Serine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Threonine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Tryptophan 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Tyrosine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +L-Valine 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 +Pyruvic_acid 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 4.56717332815963e-05 0.0 0.00288745573738021 0.00271907830075352 0.00013907509437508 5.51743930058195e-05 0.00358424038619463 0.00376914936570372 |
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| diff -r a01453baaf5e -r c0103ea608fc test-data/abundance--cell-Control-L-Cycloserine-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-Control-L-Cycloserine-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,25 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Glycine -1.0 1.0 1.0 cell [4.255576 3.417613] [2.87226 3.424984] +Hexose -1.0 1.0 1.0 cell [4.618336 3.491236] [2.947138 3.203724] +Hexose-phosphate -1.0 1.0 1.0 cell [4.108111 2.697149] [2.413296 2.655447] +L-Alanine -1.0 1.0 1.0 cell [3.302788 3.14283 ] [2.43315 3.200548] +L-Lysine -1.0 1.0 1.0 cell [5.576418 3.786704] [3.432559 3.499267] +L-Proline -1.0 1.0 1.0 cell [4.05992 3.613014] [2.83203 3.879342] +L-Serine -1.0 1.0 1.0 cell [5.329834 4.292357] [3.623779 4.074288] +L-Threonine -1.0 1.0 1.0 cell [4.997154 3.623269] [3.434891 3.45371 ] +Ile_Leu 1.0 1.0 1.0 cell [4.900535 3.337393] [3.030205 2.922865] +L-Arginine 1.0 1.0 1.0 cell [5.002539 3.168993] [3.358616 2.794746] +L-Aspartic_acid 1.0 1.0 1.0 cell [2.926178 0.604969] [1.310091 0.508822] +L-Glutamic_acid 1.0 1.0 1.0 cell [3.916821 2.30352 ] [2.203319 2.192284] +L-Glutamine 1.0 1.0 1.0 cell [3.10904 1.458991] [1.569472 1.216207] +L-Histidine 1.0 1.0 1.0 cell [5.046696 3.143408] [3.188606 2.910277] +L-Lactic_acid 1.0 1.0 1.0 cell [4.388836 3.17085 ] [2.580271 2.467079] +L-Malic_acid 1.0 1.0 1.0 cell [3.984239 2.221886] [3.288748 2.652708] +L-Methionine 1.0 1.0 1.0 cell [5.30659 3.77877] [3.589049 3.574521] +L-Phenylalanine 1.0 1.0 1.0 cell [4.846542 3.17885 ] [3.031899 2.794881] +L-Tryptophan 1.0 1.0 1.0 cell [4.92931 2.874653] [2.759392 2.666666] +L-Tyrosine 1.0 1.0 1.0 cell [5.003738 3.325451] [3.166826 2.956651] +L-Valine 1.0 1.0 1.0 cell [5.655527 4.449566] [4.032882 3.998557] +Pyruvic_acid 1.0 1.0 1.0 cell [1.408848 2.63986 ] [1.01521 2.037201] +Fructose_1,6-bisphosphate cell [ nan 0.71992] [nan nan] +Fumaric_acid cell [3.692766 1.743812] [2.397314 nan] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/abundance--med-Control-L-Cycloserine-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-Control-L-Cycloserine-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,20 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Hexose -1.0 1.0 1.0 med [17.323478 16.30882 ] [17.234918 19.00465 ] +Ile_Leu -1.0 1.0 1.0 med [16.69374 15.713286] [17.497952 18.300431] +L-Alanine -1.0 1.0 1.0 med [6.016043 5.722255] [6.847528 7.781428] +L-Asparagine -1.0 1.0 1.0 med [10.236824 8.224644] [ 9.877881 10.424269] +L-Histidine -1.0 1.0 1.0 med [27.655594 25.868636] [27.272808 28.447726] +L-Lactic_acid -1.0 1.0 1.0 med [25.499578 24.518913] [24.102561 26.366482] +L-Methionine -1.0 1.0 1.0 med [17.685546 16.454068] [18.42993 18.993209] +L-Phenylalanine -1.0 1.0 1.0 med [16.550902 15.608278] [17.382841 18.270953] +L-Proline -1.0 1.0 1.0 med [3.778766 2.810272] [4.090356 5.553318] +L-Serine -1.0 1.0 1.0 med [18.049649 16.621876] [18.097065 19.327089] +L-Threonine -1.0 1.0 1.0 med [23.81829 22.118877] [24.1371 24.713005] +L-Tyrosine -1.0 1.0 1.0 med [18.565282 17.161201] [18.880702 19.863464] +L-Valine -1.0 1.0 1.0 med [22.789674 21.740482] [23.848366 24.293696] +Glycine 1.0 1.0 1.0 med [4.11994 3.84192] [5.444741 4.334016] +Hexose-phosphate 1.0 1.0 1.0 med [7.225669 5.373172] [8.029712 6.894561] +L-Arginine 1.0 1.0 1.0 med [52.762527 50.409341] [52.519447 51.499051] +L-Lysine 1.0 1.0 1.0 med [68.280981 66.313756] [68.367814 67.499031] +L-Tryptophan 1.0 1.0 1.0 med [14.618856 12.939212] [13.272943 12.897328] +Pyruvic_acid 1.0 1.0 1.0 med [26.166366 26.254509] [27.261571 27.575891] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/example5_metadata.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example5_metadata.csv Thu Feb 15 12:51:04 2024 +0000 |
| b |
| @@ -0,0 +1,17 @@ +name_to_plot condition timepoint timenum compartment original_name +Ctrl_cell_T0-1 Control T0 0 cell MCF001089_TD01 +Ctrl_cell_T0-2 Control T0 0 cell MCF001089_TD02 +Ctrl_cell_T2h-1 Control T2h 2 cell MCF001089_TD07 +Ctrl_cell_T2h-2 Control T2h 2 cell MCF001089_TD08 +L-Cyc_cell_T0-1 L-Cycloserine T0 0 cell MCF001089_TD19 +L-Cyc_cell_T0-2 L-Cycloserine T0 0 cell MCF001089_TD20 +L-Cyc_cell_T2h-1 L-Cycloserine T2h 2 cell MCF001089_TD25 +L-Cyc_cell_T2h-2 L-Cycloserine T2h 2 cell MCF001089_TD26 +Ctrl_med_T0-1 Control T0 0 med MCF001089_TD37 +Ctrl_med_T0-2 Control T0 0 med MCF001089_TD38 +Ctrl_med_T2h-1 Control T2h 2 med MCF001089_TD43 +Ctrl_med_T2h-2 Control T2h 2 med MCF001089_TD44 +L-Cyc_med_T0-1 L-Cycloserine T0 0 med MCF001089_TD55 +L-Cyc_med_T0-2 L-Cycloserine T0 0 med MCF001089_TD56 +L-Cyc_med_T2h-1 L-Cycloserine T2h 2 med MCF001089_TD61 +L-Cyc_med_T2h-2 L-Cycloserine T2h 2 med MCF001089_TD62 |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/isotop_prop--cell--MDV-Control-L-Cycloserine--T0-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--cell--MDV-Control-L-Cycloserine--T0-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,11 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +L-Arginine -0.979871 0.000109 0.001092 cell [0.07 0.06 0.05 0.04 0.03 0.02 0.0001] [0.0001 0.02 0.03 0.04 0.05 0.06 0.07 ] +Glycine -0.973056 0.148117 0.493723 cell [0.5 0.2 0.001] [0.001 0.2 0.5 ] +L-Glutamic_acid -0.739657 0.092845 0.464226 cell [0.5 0.23 0.13 0.1 0.04 0.001] [0.001 0.04 0.1 0.13 0.23 0.5 ] +Pyruvic_acid -0.67551 0.32449 0.657105 cell [0.074833 0.1249 0.214476 0.584808] [5.84808e-01 2.14476e-01 1.00000e-04 5.00000e-04] +L-Alanine -0.671448 0.328552 0.657105 cell [7.34166e-01 2.62679e-01 1.00000e-02 1.00000e-04] [1.00e-04 1.00e-02 2.11e-01 6.99e-01] +L-Lactic_acid -0.344007 0.655993 0.937133 cell [1.0000e-04 1.0000e-04 1.1796e-02 9.8820e-01] [9.8805e-01 1.1947e-02 1.0000e-04 1.0000e-04] +L-Aspartic_acid -0.278038 0.650607 0.937133 cell [9.8645e-01 2.0000e-04 1.2380e-02 1.1310e-03 1.0000e-04] [3.16000e-04 1.71500e-03 1.49730e-02 1.89737e-01 1.00000e-04] +Fructose_1,6-bisphosphate cell [nan nan nan nan nan nan nan] [nan nan nan nan nan nan nan] +Fumaric_acid cell [nan nan nan nan nan] [ nan nan nan nan 0.000387] +L-Glutamine cell [nan nan nan nan nan nan] [2.82843e-01 5.83100e-03 9.67500e-03 1.00000e-04 6.00000e-03 2.00000e-03] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/isotop_prop--cell--MDV-Control-L-Cycloserine--T2h-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--cell--MDV-Control-L-Cycloserine--T2h-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,11 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.407405 0.592595 1.0 cell [0.244949 0.424264 0.212132 0.122474] [0.054772 0.173205 0.264575 0.273861] +L-Lactic_acid -0.344007 0.655993 1.0 cell [9.8805e-01 1.1947e-02 1.0000e-04 1.0000e-04] [1.0000e-04 1.0000e-04 1.1796e-02 9.8820e-01] +Glycine -0.187368 0.880008 1.0 cell [0.273861 0.574456 0.003162] [0.004472 0.387298 0.5 ] +L-Arginine 0.645497 0.117387 0.293467 cell [1.e-04 1.e-04 1.e-04 1.e+00 1.e-04 1.e-04 1.e-04] [0.0001 0.01 0.0001 0.01 0.0001 0.0001 0.0001] +L-Alanine 0.932835 0.067165 0.223885 cell [1.00e+00 1.00e-04 1.41e-04 6.16e-03] [7.34166e-01 2.62679e-01 1.00000e-04 1.00000e-04] +L-Aspartic_acid 0.99977 4e-06 2.1e-05 cell [0.737613 0.070846 0.125771 0.056138 0.009165] [0.747988 0.06325 0.116466 0.059249 0.012935] +L-Glutamic_acid 0.999941 0.0 0.0 cell [0.564508 0.071156 0.246995 0.059399 0.048197 0.009499] [0.556649 0.070137 0.249195 0.06265 0.0507 0.010588] +Fructose_1,6-bisphosphate cell [0.01 0.0001 0.0001 0.0001 0.01 0.0001 0.0001] [ nan 0.000316 nan nan 0.01 nan nan] +Fumaric_acid cell [9.98949e-01 1.00000e-04 6.56000e-04 2.45000e-04 4.00000e-04] [nan nan nan nan nan] +L-Glutamine cell [nan nan nan nan nan nan] [nan nan nan nan nan nan] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/isotop_prop--cell--MDV-T2h-T0--Control-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--cell--MDV-T2h-T0--Control-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,11 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.710557 0.289443 0.723607 cell [0.244949 0.424264 0.212132 0.122474] [0.074833 0.1249 0.214476 0.584808] +L-Lactic_acid -0.344007 0.655993 1.0 cell [9.8805e-01 1.1947e-02 1.0000e-04 1.0000e-04] [1.0000e-04 1.0000e-04 1.1796e-02 9.8820e-01] +L-Arginine 0.025903 0.956041 1.0 cell [1.e-04 1.e-04 1.e-04 1.e+00 1.e-04 1.e-04 1.e-04] [0.07 0.06 0.05 0.04 0.03 0.02 0.0001] +Glycine 0.368192 0.759953 1.0 cell [0.273861 0.574456 0.003162] [0.5 0.2 0.001] +L-Glutamic_acid 0.895139 0.015917 0.079587 cell [0.564508 0.071156 0.246995 0.059399 0.048197 0.009499] [0.5 0.23 0.13 0.1 0.04 0.001] +L-Alanine 0.934368 0.065632 0.218775 cell [1.00e+00 1.00e-04 1.41e-04 6.16e-03] [7.34166e-01 2.62679e-01 1.00000e-02 1.00000e-04] +L-Aspartic_acid 0.99186 0.00088 0.008805 cell [0.737613 0.070846 0.125771 0.056138 0.009165] [9.8645e-01 2.0000e-04 1.2380e-02 1.1310e-03 1.0000e-04] +Fructose_1,6-bisphosphate cell [0.01 0.0001 0.0001 0.0001 0.01 0.0001 0.0001] [nan nan nan nan nan nan nan] +Fumaric_acid cell [9.98949e-01 1.00000e-04 6.56000e-04 2.45000e-04 4.00000e-04] [nan nan nan nan nan] +L-Glutamine cell [nan nan nan nan nan nan] [nan nan nan nan nan nan] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/isotop_prop--cell--MDV-T2h-T0--L-Cycloserine-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--cell--MDV-T2h-T0--L-Cycloserine-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,11 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.995621 0.004379 0.043786 cell [0.054772 0.173205 0.264575 0.273861] [5.84808e-01 2.14476e-01 1.00000e-04 5.00000e-04] +L-Alanine -0.666339 0.333661 0.834151 cell [7.34166e-01 2.62679e-01 1.00000e-04 1.00000e-04] [1.00e-04 1.00e-02 2.11e-01 6.99e-01] +L-Glutamic_acid -0.600809 0.207224 0.834151 cell [0.556649 0.070137 0.249195 0.06265 0.0507 0.010588] [0.001 0.04 0.1 0.13 0.23 0.5 ] +L-Lactic_acid -0.344007 0.655993 0.938087 cell [1.0000e-04 1.0000e-04 1.1796e-02 9.8820e-01] [9.8805e-01 1.1947e-02 1.0000e-04 1.0000e-04] +L-Aspartic_acid -0.273092 0.656661 0.938087 cell [0.747988 0.06325 0.116466 0.059249 0.012935] [3.16000e-04 1.71500e-03 1.49730e-02 1.89737e-01 1.00000e-04] +L-Arginine -0.243607 0.598601 0.938087 cell [0.0001 0.01 0.0001 0.01 0.0001 0.0001 0.0001] [0.0001 0.02 0.03 0.04 0.05 0.06 0.07 ] +Glycine 0.912581 0.268172 0.834151 cell [0.004472 0.387298 0.5 ] [0.001 0.2 0.5 ] +Fructose_1,6-bisphosphate cell [ nan 0.000316 nan nan 0.01 nan nan] [nan nan nan nan nan nan nan] +Fumaric_acid cell [nan nan nan nan nan] [ nan nan nan nan 0.000387] +L-Glutamine cell [nan nan nan nan nan nan] [2.82843e-01 5.83100e-03 9.67500e-03 1.00000e-04 6.00000e-03 2.00000e-03] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/isotop_prop--med--MDV-Control-L-Cycloserine--T0-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--med--MDV-Control-L-Cycloserine--T0-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,6 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.566976 0.433024 0.855516 med [0.1 0.1 0.214476 0.584808] [0.584808 0.214476 0.1 0.1 ] +L-Arginine 0.3 0.51331 0.855516 med [0.01 0.0001 0.0001 0.01 0.0001 0.0001 0.0001] [0.0001 0.0001 0.01 0.01 0.0001 0.0001 0.0001] +L-Lactic_acid 0.999998 2e-06 1e-05 med [1.6137e-02 2.0000e-04 1.2050e-02 9.7160e-01] [1.4087e-02 2.0000e-04 1.2050e-02 9.7365e-01] +Glycine med [nan nan nan] [nan nan nan] +L-Alanine med [0.0001] [0.0001] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/isotop_prop--med--MDV-Control-L-Cycloserine--T2h-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--med--MDV-Control-L-Cycloserine--T2h-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,6 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.407405 0.592595 0.987658 med [0.244949 0.424264 0.212132 0.122474] [0.054772 0.173205 0.264575 0.273861] +L-Arginine 0.645497 0.117387 0.293467 med [1.e-04 1.e-04 1.e-04 1.e+00 1.e-04 1.e-04 1.e-04] [0.0001 0.01 0.0001 0.01 0.0001 0.0001 0.0001] +L-Lactic_acid 0.999999 1e-06 5e-06 med [1.8178e-02 2.0000e-04 1.2050e-02 9.6955e-01] [1.94380e-02 1.41000e-04 1.18500e-02 9.68195e-01] +Glycine med [nan nan nan] [nan nan nan] +L-Alanine med [0.000608] [0.0001] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/isotop_prop--med--MDV-T2h-T0--Control-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--med--MDV-T2h-T0--Control-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,6 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.764727 0.235273 0.392122 med [0.244949 0.424264 0.212132 0.122474] [0.1 0.1 0.214476 0.584808] +L-Arginine 0.645497 0.117387 0.293467 med [1.e-04 1.e-04 1.e-04 1.e+00 1.e-04 1.e-04 1.e-04] [0.01 0.0001 0.0001 0.01 0.0001 0.0001 0.0001] +L-Lactic_acid 0.999998 2e-06 1e-05 med [1.8178e-02 2.0000e-04 1.2050e-02 9.6955e-01] [1.6137e-02 2.0000e-04 1.2050e-02 9.7160e-01] +Glycine med [nan nan nan] [nan nan nan] +L-Alanine med [0.000608] [0.0001] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/isotop_prop--med--MDV-T2h-T0--L-Cycloserine-pearson.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/isotop_prop--med--MDV-T2h-T0--L-Cycloserine-pearson.tsv Thu Feb 15 12:51:04 2024 +0000 |
| [ |
| @@ -0,0 +1,6 @@ +metabolite correlation_coefficient pvalue padj compartment gmean_arr_1 gmean_arr_2 +Pyruvic_acid -0.974457 0.025543 0.063858 med [0.054772 0.173205 0.264575 0.273861] [0.584808 0.214476 0.1 0.1 ] +L-Arginine 0.3 0.51331 0.855516 med [0.0001 0.01 0.0001 0.01 0.0001 0.0001 0.0001] [0.0001 0.0001 0.01 0.01 0.0001 0.0001 0.0001] +L-Lactic_acid 0.999985 1.5e-05 7.4e-05 med [1.94380e-02 1.41000e-04 1.18500e-02 9.68195e-01] [1.4087e-02 2.0000e-04 1.2050e-02 9.7365e-01] +Glycine med [nan nan nan] [nan nan nan] +L-Alanine med [0.0001] [0.0001] |
| b |
| diff -r a01453baaf5e -r c0103ea608fc test-data/rawAbundances_5.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rawAbundances_5.csv Thu Feb 15 12:51:04 2024 +0000 |
| b |
| @@ -0,0 +1,26 @@ +ID MCF001089_TD01 MCF001089_TD02 MCF001089_TD07 MCF001089_TD08 MCF001089_TD19 MCF001089_TD20 MCF001089_TD25 MCF001089_TD26 MCF001089_TD37 MCF001089_TD38 MCF001089_TD43 MCF001089_TD44 MCF001089_TD55 MCF001089_TD56 MCF001089_TD61 MCF001089_TD62 +Fructose_1,6-bisphosphate 81.46798666666666 31.66305777777778 488.62223666666665 30.88032133333333 108.58193666666666 +Fumaric_acid 1765.8621555555562 2350.101706666667 565.6100944444463 1636.1451616666689 1112.7411533333332 1571.7939723809532 2082.227511666667 +Glycine 31339.848144444444 19953.502358333335 15011.070372222222 26867.879408333334 20173.435886666666 14121.041376190477 15741.494772222224 25731.819858333336 21082398.016666666 20528546.116666667 19650482.416666664 19152242.516666666 35768152.41666667 21132662.81666667 21540901.71666667 22233782.916666664 +Hexose 15263.525582222223 10653.204421666667 7620.2662477777785 12194.176071666667 9284.639177333334 7131.811518095239 6702.562494444444 11674.364736666666 23812934.643333334 24242428.643333334 22336054.643333334 22906432.643333334 23957348.643333334 23850557.643333334 26889340.643333334 25837975.643333334 +Hexose-phosphate 556790.6730444445 410704.96478333336 215369.08985555556 457681.9897833334 337548.2038266667 233788.3998761905 229354.86985555556 416586.1147833334 1792538.5666666667 1790949.5666666667 1218328.5666666667 1457111.5666666667 2069691.5666666667 1915534.5666666667 1684708.5666666667 1734938.5666666667 +Ile_Leu 723695.6614222223 871117.5290666667 433211.3440444445 674932.9420666667 545783.4088533333 441641.19203809527 354037.3863777778 633452.6395666667 2111708660.1333334 2203285239.133333 2037012929.1333334 2023660803.1333334 2311992779.133333 2210982973.133333 2389754947.133333 2339735205.133333 +L-Alanine 14581.8738 7816.563399999999 7056.1678999999995 14626.51065 9781.123839999998 6324.36291142857 8061.856666666667 13276.4346 1548485.77 1701510.73 1309197.7400000002 1820745.4700000002 1935085.62 1763954.77 1931224.9000000004 2282473.1300000004 +L-Arginine 5680.366466666666 7466.331200000001 4182.386200000001 4069.3133000000003 5139.229840000001 3719.8487428571434 2943.6414666666674 4496.78815 76704557.1 76562817.1 74284491.1 72162535.1 76269336.1 76291863.1 74652772.1 74944609.1 +L-Asparagine 3617749.87 3435790.2 2756887.13 2910381.68 3513705.7 3293797.9 3311566.8 3892175.2 +L-Aspartic_acid 71486.78267333333 55376.312 8361.739503333332 20235.678005 34321.611392 23119.754611428572 7664.626003333333 15616.709855000001 +L-Glutamic_acid 139191.37992666668 104355.48684499999 46972.50566333334 106954.896995 82261.28531600001 55875.258682857144 47872.660330000006 95053.066995 +L-Glutamine 18606.32958888889 9863.261441666667 4512.041427777778 8956.960391666667 8701.497033333335 5374.547080952381 4094.7460777777783 6858.299791666668 +L-Histidine 16420.387355555555 15111.119316666667 8215.772844444444 11717.067916666667 12255.282253333333 8082.469038095238 7269.836411111111 11350.365116666668 66137818.63333333 67607708.63333334 63420421.63333333 61687625.63333333 64943662.63333333 66958084.63333333 67970373.63333334 69607422.63333334 +L-Lactic_acid 1073607.0293955556 1722584.2720466666 973301.2546977778 991816.0770466666 879872.2496373333 726504.4068838095 614361.0746977777 951194.5220466666 9322737799.093334 9302697744.093334 9196079213.093334 8719390692.093334 8901197393.093334 8704911808.093334 9400722189.093334 9863466762.093334 +L-Lysine 11537.73680888889 13806.366056666666 8333.777904444445 8813.939856666668 9173.407525333334 6579.528718095239 6643.038094444445 9442.279106666667 117443154.71333334 121027940.71333334 115723826.71333334 115850611.09333333 119744345.59333333 119004184.71333334 118584270.71333334 117133694.71333334 +L-Malic_acid 83435.18658666659 84111.08978999997 28512.006359999974 76546.89803999996 79766.01795199995 59945.28643999999 37016.17602666664 84042.47953999996 +L-Methionine 50953.09172444445 49086.99679333334 28047.987862222224 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