| Next changeset 1:dc199abf3db4 (2024-01-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit abca848510cb4ac8d09d95634147626ea578cdf0 |
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added:
dimet_differential_analysis.xml macros.xml test-data/AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg test-data/AbundanceCorrected.csv test-data/CENTRAL_CARBON_METABOLISM-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg test-data/CorrectedIsotopologues_reduced.csv test-data/DEG_comparison_1.csv test-data/FracContribution_C.csv test-data/Isotopologues_cell-Fructose_1,6-bisphosphate.svg test-data/Isotopologues_cell-L-Aspartic_acid.svg test-data/Isotopologues_cell-L-Glutamic_acid.svg test-data/Isotopologues_cell-L-Glutamine.svg test-data/Isotopologues_cell-L-Lactic_acid.svg test-data/Isotopologues_cell-L-Lysine.svg test-data/Isotopologues_cell-L-Proline.svg test-data/Isotopologues_cell-L-Serine.svg test-data/Isotopologues_med-L-Lactic_acid.svg test-data/Isotopologues_med-L-Lysine.svg test-data/Isotopologues_med-L-Proline.svg test-data/Isotopologues_med-L-Serine.svg test-data/abundance--cell--multigroup.tsv test-data/abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv test-data/abundance--cell-Control-T2h-Control-T0-Tt.tsv test-data/abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv test-data/abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv test-data/abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv test-data/abundance--med-Control-T2h-Control-T0-Tt.tsv test-data/abundance--med-Control-T2h-L-Cycloserine-T2h-Tt.tsv test-data/abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv test-data/abundances--T0--cell--label-n_pc.svg test-data/abundances--T0--cell--label-y_pc.svg test-data/abundances--T0--cell_pc.csv test-data/abundances--T0--cell_var.csv test-data/abundances--T0--cell_var.svg test-data/abundances--T0--med--label-n_pc.svg test-data/abundances--T0--med--label-y_pc.svg test-data/abundances--T0--med_pc.csv test-data/abundances--T0--med_var.csv test-data/abundances--T0--med_var.svg test-data/abundances--T2h--cell--label-n_pc.svg test-data/abundances--T2h--cell--label-y_pc.svg test-data/abundances--T2h--cell_pc.csv test-data/abundances--T2h--cell_var.csv test-data/abundances--T2h--cell_var.svg test-data/abundances--T2h--med--label-n_pc.svg test-data/abundances--T2h--med--label-y_pc.svg test-data/abundances--T2h--med_pc.csv test-data/abundances--T2h--med_var.csv test-data/abundances--T2h--med_var.svg test-data/abundances--cell--label-n_pc.svg test-data/abundances--cell--label-y_pc.svg test-data/abundances--cell_pc.csv test-data/abundances--cell_var.csv test-data/abundances--cell_var.svg test-data/abundances--med--label-n_pc.svg test-data/abundances--med--label-y_pc.svg test-data/abundances--med_pc.csv test-data/abundances--med_var.csv test-data/abundances--med_var.svg test-data/bars_endo_Fru1P-total_abundance.svg test-data/example1_metadata.csv test-data/example2_metadata.csv test-data/example3_metadata.csv test-data/legend-abundances-cell.svg test-data/legend.svg test-data/legend_isotopologues_stackedbars.svg test-data/mean_enrichment-cell-Fumaric_acid.svg test-data/mean_enrichment-cell-Glycine.svg test-data/mean_enrichment-cell-L-Proline.svg test-data/mean_enrichment-med-Fumaric_acid.svg test-data/mean_enrichment-med-Glycine.svg test-data/mean_enrichment-med-L-Proline.svg test-data/pathways_kegg_metabolites.csv test-data/pathways_kegg_transcripts.csv test-data/rawAbundances.csv test-data/rawAbundances3.csv |
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| diff -r 000000000000 -r c46d33411495 dimet_differential_analysis.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dimet_differential_analysis.xml Tue Oct 10 11:52:44 2023 +0000 |
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| b'@@ -0,0 +1,296 @@\n+<tool id="dimet_@EXECUTABLE@" name="dimet @TOOL_LABEL@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">\n+ <description>\n+ Differential analysis of tracer metabolomics data comparing two groups (by DIMet)\n+ </description>\n+ <macros>\n+ <token name="@TOOL_LABEL@">differential analysis</token>\n+ <token name="@EXECUTABLE@">differential_analysis</token>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ @INIT_CONFIG@\n+ @INIT_DIFF_ANALYSIS@\n+ @INIT_STAT_TEST@\n+ @INIT_GROUPS@\n+ @INIT_COMPARISONS@\n+ HYDRA_FULL_ERROR=1 python -m dimet\n+ -cp \'$__new_file_path__/config\'\n+ \'++hydra.run.dir=differential_analysis\'\n+ \'++figure_path=figures\'\n+ \'++table_path=tables\'\n+ \'++analysis={\n+ dataset:{\n+ _target_: dimet.data.DatasetConfig,\n+ name: "I am a synthetic data example"\n+ },\n+ method:{\n+ _target_: dimet.method.DifferentialAnalysisConfig,\n+ label: "differential_analysis",\n+ name: "Pairwise computation of statistical differences",\n+ draw_ellipses: null,\n+ run_iris_demo: false\n+ },\n+ label: differential-analysis-example2\n+ }\'\n+ \'++analysis.method.qualityDistanceOverSpan=\'${qualityDistanceOverSpan}\'\'\n+ \'++analysis.dataset.label=\'\n+ \'++analysis.timepoints=${timepoints}\'\n+ \'++analysis.comparisons=${comparisons}\'\n+ \'++analysis.method.statistical_test=${statistical_test}\'\n+ \'++analysis.method.grouping=${groups}\'\n+ \'++analysis.method.correction_method=${correction_method}\'\n+ \'++analysis.method.impute_values=${impute_values}\'\n+ \'++analysis.statistical_test=${statistical_test}\'\n+ \'++analysis.dataset.subfolder=\'\n+ \'++analysis.dataset.conditions=${conds}\'\n+ #if $metadata_path:\n+ \'++analysis.dataset.metadata=metadata\'\n+ #end if\n+ #if str( $data_input.data_input_selector ) == "abundance":\n+ #if $data_input.abundance_file:\n+ \'++analysis.dataset.abundances=abundance\'\n+ #end if\n+ #elif str( $data_input.data_input_selector ) == "mean_enrichment":\n+ #if $data_input.me_or_frac_contrib_file:\n+ \'++analysis.dataset.mean_enrichment=me_or_frac_contrib\'\n+ #end if\n+ #elif str( $data_input.data_input_selector ) == "isotop_prop":\n+ #if $data_input.isotop_prop_file:\n+ \'++analysis.dataset.isotopologue_proportions=isotop_prop\'\n+ #end if\n+ #else\n+ #if $data_input.isotop_abs_file:\n+ \'++analysis.dataset.isotopologues=isotop_abs\'\n+ #end if\n+ #end if\n+ @REMOVE_CONFIG@\n+ ]]></command>\n+ <inputs>\n+ <expand macro="input_parameters_diff_analysis"/>\n+ <expand macro="conditions"/>\n+ <expand macro="timepoint"/>\n+ <expand macro="correction_method"/>\n+ <param name="qualityDistanceOverSpan" type="float" min="-1.0" max="-0.1" value="-0.3" label="quality Distance Over Span" help="Default value is -0.3."/>\n+ </inputs>\n+\n+ <outputs>\n+ <collection name="report" type="list">\n+ <discover_datasets pattern="__designation__" directory="tables" format="tabular"/>\n+ </collection>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="data_input_selector" value="abundance" />\n+ <param name="abundance_file" ftype="tabular" value="rawAbundances.csv"/>\n+ <param name="metadata_path" ftype="tabular" value="example2_metadata.csv"/>\n+ <param name="correction_method" value="bonferroni"/>\n+ <param name="stat_test" value="Tt"/>\n+ <param name="qualityDistanceOverSpan" value="-0.3"/>\n+ <param'..b' cell MCF001089_TD07\n+ Tumoral_cell_T24-2 Tumoral T24 24 cell MCF001089_TD08\n+ Tumoral_cell_T24-3 Tumoral T24 24 cell MCF001090_TD01\n+ Control_med_T24-1 Control T24 24 med MCF001090_TD02\n+ Control_med_T24-2 Control T24 24 med MCF001090_TD03\n+ Tumoral_med_T24-1 Tumoral T24 24 med MCF001090_TD04\n+ Tumoral_med_T24-2 Tumoral T24 24 med MCF001090_TD05\n+ Control_med_T0-1 Control T0 0 med MCF001090_TD06\n+ Tumoral_med_T0-1 Tumoral T0 0 med MCF001090_TD07\n+ Tumoral_med_T0-2 Tumoral T0 0 med MCF001090_TD08\n+ ==================== =============== ============= ============ ================ =================\n+\n+\n+The column **original_name** must have the names of the samples as given in your data.\n+\n+The column **name_to_plot** must have the names as you want them to be (or set identical to original_name if you prefer). To set names that\n+are meaningful is a better choice, as we will take them to display the results.\n+\n+The column **timenum** must contain only the numeric part of the timepoint, for example 2,0, 10, 100 (this means, without letters ("T", "t", "s", "h" etc)\n+nor any other symbol). Make sure these time numbers are in the same units (but do not write the units here!).\n+\n+The column **compartment** is an abbreviation, coined by you, for the compartments. This will be used for the results\' files names: the longer the\n+compartments names are, the longer the output files\' names! Please pick short and clear abbreviations to fill this column.\n+\n+\n+**Running the analysis**\n+\n+You can precise how you want your analysis to be executed, with the parameters:\n+\n+- **conditions**: the conditions present in your data, specifying in first place your CONTROL condition (this ordering is crucial to make the comparisons in a coherent sense).\n+\n+- **comparisons** : the pairs of [condition, timepoint] groups to compare\n+\n+- **datatypes** : the measures type(s) that you want to run\n+\n+- **statistical_test** : choose, by type of measure, the specific statistical test to be applied.\n+\n+ Kruskal-Wallis, Mann-Whitney, Wilcoxon\xe2\x80\x99s signed rank test, Wilcoxon\xe2\x80\x99s rank sum test\n+ t-test, and permutation test are currently offered (we use the trusted functions from scipy library https://docs.scipy.org/doc/scipy/reference/stats.html).\n+\n+For the permutation test, we have established as test statistic, the absolute difference of geometric means of the two compared groups.\n+\n+- **qualityDistanceOverSpan**: a normalized distance between the intervals of values of the compared groups, that is the cutoff for\n+\n+considering a minimal acceptable "separation", and therefore, to be suitable for statistical testing. A \'distance/span\' == 1 is a perfect separation,\n+whereas if \'distance/span\' < 0 there is no separation.\n+To use with caution in case of important dispersion of your intra-group values. Default is -0.3 (not stringent)\n+\n+- **correction_method** : one of the methods for multiple testing correction available in statsmodels library (bonferroni, fdr_bh, sidak, among others, see https://www.statsmodels.org/dev/generated/statsmodels.stats.multitest.multipletests.html).\n+\n+There exist hints on use that will guide you, next to the parameters.\n+\n+\n+**Available data for testing**\n+\n+You can test our tool with the data from our manuscript https://zenodo.org/record/8378887 (the pertinent\n+files for you are located in the subfolders inside the data folder).\n+You can also use the minimal data examples from https://zenodo.org/record/8380706\n+\n+ ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r 000000000000 -r c46d33411495 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Tue Oct 10 11:52:44 2023 +0000 |
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| b'@@ -0,0 +1,778 @@\n+<macros>\n+ <token name="@TOOL_VERSION@">0.1.4</token>\n+ <token name="@VERSION_SUFFIX@">0</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">\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+ </xml>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="bibtex">\n+ @software{Galvis_Rodriguez_DIMet,\n+ author = {Galvis Rodriguez, Johanna and Guyon, Joris and Dartigues, Benjamin and Specque, Florian and Daubon, Thomas and Karkar, Slim and Nikolski, Macha},\n+ license = {MIT},\n+ title = {{DIMet}},\n+ url = {https://github.com/cbib/DIMet}\n+ }\n+\n+ </citation>\n+ </citations>\n+\n+ </xml>\n+ <xml name="metadata_file_macros">\n+ <param name="metadata_path" type="data" format="tabular" label="metadata file" help="The metadata, a unique file with the description of the samples in your measures\' files. This is compulsory, see section Metadata File Information."/>\n+ </xml>\n+ <xml name="abundance_file_macros">\n+ <param name="abundance_file" type="data" format="tabular" label="Metabolite abundance file" help="The total abundances file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns correspond to the samples - The rows correspond to the metabolites - The values must be tab separated, with the first row containing the sample/column labels. (see help below for more details)"/>\n+ </xml>\n+ <xml name="enrichment_file_macros">\n+ <param name="me_or_frac_contrib_file" type="data" format="tabular" label="Metabolite enrichment file" help="The mean enrichment file must be organized as a matrix: - The first column must contain Metabolite IDs that are unique (not repeated) within the file. - The rest of the columns corres'..b' #set $ctrl=str($co)\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($co)))\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($tp)))\n+ #else:\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($co)))\n+ $sub_comparisons.append(re.sub(\'"\', \'\', str($tp)))\n+\n+ #end if\n+ $comparisons.append($sub_comparisons)\n+ #end for\n+ #end for\n+ ]]></token>\n+ <token name="@INIT_CONDITIONS_TIMECOURSE@"><![CDATA[\n+ #import re\n+ #set $conds = list()\n+ #for $co in $conditions:\n+ $conds.append(re.sub(\'"\', \'\', str($co)))\n+ #end for\n+\n+ ]]></token>\n+ <token name="@INIT_COMPARISONS@"><![CDATA[\n+ #import re\n+ #set $conds = list()\n+ #for $co in $conditions:\n+ $conds.append(re.sub(\'"\', \'\', str($co)))\n+ #end for\n+ #set $timepoints = list()\n+ #for $tp in $timepoint:\n+ $timepoints.append(re.sub(\'"\', \'\', str($tp)))\n+ #end for\n+\n+ #set $comparisons = list()\n+ #if len($conds) > 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+ #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($conds) > 0:\n+ #if len($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+ #import subprocess\n+ #set $transcripts = list()\n+\n+ #for $i, $s in enumerate($deg_list)\n+ #set $cpt = str($i+1)\n+ $transcripts.append(re.sub(\'"\', \'\', "DEG_comparison"+str($i+1)))\n+ #set $deg_one_values = os.fsdecode(subprocess.check_output(\'head -n1 \' + str($s.input) + \'| cut -f\' + str($s.valuecol), shell=True))\n+ #set $deg_one_id = os.fsdecode(subprocess.check_output(\'head -n1 \' + str($s.input) + \'| cut -f\' + str($s.idcol), shell=True))\n+ #end for\n+ ]]></token>\n+ <token name="@INIT_PATHWAYS@"><![CDATA[\n+ #set $pathways = {}\n+ #if $path_kegg_metabolites:\n+ #silent $pathways[\'metabolites\']=\'pathways_kegg_metabolites\'\n+ #end if\n+ #if $path_kegg_transcripts:\n+ #silent $pathways[\'transcripts\']=\'pathways_kegg_transcripts\'\n+ #end if\n+ ]]></token>\n+</macros>\n' |
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| diff -r 000000000000 -r c46d33411495 test-data/AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/AMINOACIDS-Control-T0-L-Cycloserine-T0--DEG_comparison1-abundances-cell.svg Tue Oct 10 11:52:44 2023 +0000 |
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| diff -r 000000000000 -r c46d33411495 test-data/CorrectedIsotopologues_reduced.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/CorrectedIsotopologues_reduced.csv Tue Oct 10 11:52:44 2023 +0000 |
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| @@ -0,0 +1,46 @@ +"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 1 1 1 1 +"Fructose_1,6-bisphosphate_m+1" 0 0 0 0 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 0 0 0 0 +"Fructose_1,6-bisphosphate_m+5" 0 0 0 0 0 +"Fructose_1,6-bisphosphate_m+6" 0 0 0 0 0 +"L-Aspartic_acid_m+0" 0.9863 0.9866 0.745 0.7303 0.982 0.9831 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 0.0004 0.0008 0.0589 0.0596 +"L-Aspartic_acid_m+4" 0 0.0001 0.007 0.012 0.0003 0 0.0117 0.0143 +"L-Glutamic_acid_m+0" 0.9491 0.9486 0.5577 0.5714 0.9508 0.9458 0.5577 0.5556 +"L-Glutamic_acid_m+1" 0.0103 0.0095 0.0737 0.0687 0.0084 0.0109 0.0715 0.0688 +"L-Glutamic_acid_m+2" 0.0399 0.0409 0.2485 0.2455 0.0387 0.0408 0.2477 0.2507 +"L-Glutamic_acid_m+3" 0 0.0004 0.0619 0.057 0.0006 0.001 0.0628 0.0625 +"L-Glutamic_acid_m+4" 0.0008 0.0006 0.0487 0.0477 0.0015 0.0015 0.0508 0.0506 +"L-Glutamic_acid_m+5" 0 0 0.0094 0.0096 0 0 0.0095 0.0118 +"L-Glutamine_m+0" 1 1 0.7483 0.7005 0.997 0.9986 0.7153 0.6673 +"L-Glutamine_m+1" 0 0 0.0347 0.0402 0 0 0.0424 0.0526 +"L-Glutamine_m+2" 0.01 0.0104 0.1482 0.1693 0.009 0.0104 0.1757 0.1919 +"L-Glutamine_m+3" 0 0 0.0371 0.049 0 0 0.0363 0.043 +"L-Glutamine_m+4" 0 0 0.0263 0.0341 0 0 0.0268 0.0374 +"L-Glutamine_m+5" 0 0 0.0053 0.007 0 0 0.0034 0.0078 +"L-Lactic_acid_m+0" 0 0 0 0 0 0 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 0 0 0 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 0.0122 0.0117 0.012 0.012 0.0116 0.0113 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 0.9878 0.9883 0.988 0.988 0.9884 0.9887 0.9723 0.9709 0.9704 0.9687 0.9731 0.9742 0.9651 0.9713 +"L-Lysine_m+0" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +"L-Lysine_m+1" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Lysine_m+2" 0.0015 0.0004 0.0006 0.001 0.0006 0.0009 0.0018 0.0008 0 0 0 0 0 0 0 0 +"L-Lysine_m+3" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Lysine_m+4" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Lysine_m+5" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Lysine_m+6" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Proline_m+0" 0.9717 0.9719 0.9461 0.95 0.9813 0.9779 0.9602 0.9617 0.9939 0.9872 0.9545 1 1 1 0.9869 1 +"L-Proline_m+1" 0.0296 0.0306 0.0279 0.0284 0.0208 0.0244 0.0167 0.0061 0.0076 0.0147 0.0488 0 0 0 0.0149 0.0013 +"L-Proline_m+2" 0 0 0.0248 0.0213 0 0 0.0214 0.0302 0 0 0 0 0 0 0 0 +"L-Proline_m+3" 0 0 0 0 0 0 0 0.001 0 0 0.0001 0 0 0 0 0 +"L-Proline_m+4" 0 0 0.0021 0.0011 0 0 0.0025 0.0009 0 0 0 0 0 0 0 0 +"L-Proline_m+5" 0.0012 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Serine_m+0" 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 +"L-Serine_m+1" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Serine_m+2" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +"L-Serine_m+3" 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/DEG_comparison_1.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/DEG_comparison_1.csv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,22 @@ +"Column_1" "external_gene_name" "log2FoldChange" +"m" "ALDOA" 4 +"n" "GPI" -4 +"o" "PCK1" 3.5 +"p" "PGAM1" -2 +"y" "PKM" 0 +"r" "IDH1" 1 +"I" "MDH2" 1 +"k" "PC" -3 +"k" "SDHA" 4 +"k" "SUCLG1" -4 +"k" "SUCLG2" 3.5 +"k" "ADSS1" -2 +"k" "AGXT" 0 +"k" "ASL" 1 +"k" "ASNS" 1 +"k" "ASPA" -3 +"k" "GAD1" 0.7 +"k" "GLS" -1.8 +"k" "GLUD1" 2 +"k" "GAD1" -0.5 +"k" "GLUD2" 2.7 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/FracContribution_C.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FracContribution_C.csv Tue Oct 10 11:52:44 2023 +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 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 000000000000 -r c46d33411495 test-data/abundance--cell--multigroup.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell--multigroup.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,6 @@ +metabolite Ctrl_cell_T0h-1 Ctrl_cell_T0h-2 Ctrl_cell_T0h-3 Cond1_cell_T0h-1 Cond1_cell_T0h-2 Cond1_cell_T0h-3 Cond2_cell_T0h-1 Cond2_cell_T0h-2 Cond2_cell_T0h-3 Ctrl_cell_T2h-1 Ctrl_cell_T2h-2 Ctrl_cell_T2h-3 Cond1_cell_T2h-1 Cond1_cell_T2h-2 Cond1_cell_T2h-3 Cond2_cell_T2h-1 Cond2_cell_T2h-2 Cond2_cell_T2h-3 pvalue padj +Glycine 0.002519 0.003212 0.002011 0.009304 0.010108 0.014663 2.87541 1.698859 1.731678 0.00015 0.000175 9.8e-05 4.5e-05 1.579707 5.3e-05 1.787379 2.109744 2.1255 0.018127 0.090635 +Hexose 0.001174 0.00082 0.001356 0.000516 0.000519 0.000437 1.843131 1.834915 2.0687 0.000169 0.000253 0.000164 1.865063 1.718398 1.76228 1.987815 2.449479 2.241466 0.006794 0.033971 +L-Arginine 0.000151 0.000198 0.000111 7.8e-05 0.00012 2.038458 2.026891 2.02749 1.983931 0.000108 0.000137 9.9e-05 2.034691 1.974143 1.917751 1.991686 0.167953 0.839766 +L-Glutamine 1.58483 1.81629 1.751614 0.754035 0.894641 3.490867 3.443824 2.831176 +L-Tryptophan 6.3e-05 7.3e-05 7e-05 0.000491 0.000499 4.483307 0.344618 0.318892 0.313476 4e-05 4.5e-05 3.2e-05 0.369116 0.35728 0.292317 0.331011 0.300477 0.331022 0.030637 0.153184 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-Control-T0-L-Cycloserine-T0-Tt.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,25 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_cell_T0-1 Ctrl_cell_T0-2 L-Cyc_cell_T0-1 L-Cyc_cell_T0-2 gmean_1 gmean_2 +L-Tyrosine 0.659969 0.044578 1.0 0.544 1.580048 0 0 1.346502 2.475187 cell 5.059224 5.449813 3.712722 2.974626 5.250888 3.323245 +L-Methionine 0.564183 0.075348 1.0 0.488153 1.47855 0 0 1.21324 2.485367 cell 5.928871 5.711734 4.498494 3.443504 5.81929 3.935808 +L-Aspartic_acid 1.159351 0.071437 1.0 0.435311 2.23357 0 0 1.126485 2.587769 cell 3.824739 2.962785 1.8363 1.23697 3.366286 1.507132 +Ile_Leu 0.693524 0.078103 1.0 0.414254 1.617229 0 0 1.080144 2.607445 cell 4.393714 5.288745 3.31357 2.6813 4.820501 2.980717 +L-Tryptophan 0.837035 0.077877 1.0 0.411565 1.786375 0 0 1.07544 2.613053 cell 3.918551 4.59966 2.843111 1.986607 4.245468 2.376582 +L-Phenylalanine 0.676734 0.082439 1.0 0.397203 1.598517 0 0 1.043392 2.62685 cell 4.492276 5.358136 3.448884 2.731286 4.906142 3.069184 +L-Histidine 0.662413 0.124722 1.0 0.342512 1.582728 0 0 0.893231 2.607882 cell 5.135867 4.726362 3.833131 2.527985 4.926862 3.112892 +L-Lysine 0.700054 0.108484 1.0 0.32716 1.624566 0 0 0.879075 2.68699 cell 4.289814 5.133306 3.410739 2.446316 4.692646 2.888554 +L-Valine 0.48785 0.113542 1.0 0.317079 1.402354 0 0 0.853637 2.692194 cell 6.655174 5.844043 4.990406 3.96298 6.236435 4.44712 +L-Glutamic_acid 0.830004 0.137338 1.0 0.265185 1.777691 0 0 0.723262 2.727386 cell 4.556485 3.416118 2.692856 1.829099 3.945312 2.219347 +L-Serine 0.556596 0.152386 1.0 0.23191 1.470794 0 0 0.638261 2.752194 cell 5.905558 4.753595 4.115334 3.153364 5.298361 3.602381 +Hexose-phosphate 0.76747 0.157597 1.0 0.22649 1.702282 0 0 0.62225 2.747362 cell 4.735898 3.493336 2.871086 1.988536 4.067442 2.389405 +L-Proline 0.519615 0.177905 1.0 0.223644 1.433572 0 0 0.601013 2.687365 cell 6.102914 4.603201 4.002188 3.415549 5.300277 3.697252 +L-Lactic_acid 0.766316 0.216319 1.0 0.194497 1.70092 0 0 0.51042 2.624306 cell 2.828561 4.538379 2.318141 1.914073 3.582887 2.10644 +Hexose 0.648059 0.202852 1.0 0.1683 1.567058 0 0 0.459334 2.729259 cell 5.122919 3.575551 3.116217 2.39366 4.279867 2.731147 +Fumaric_acid 0.623283 0.19388 1.0 0.156841 1.540376 0 0 0.437164 2.787315 cell 3.977834 5.293909 2.506594 3.54067 4.588931 2.979098 +L-Malic_acid 0.276766 0.295582 1.0 0.151833 1.211476 0 0 0.371422 2.446251 cell 8.445961 8.514381 8.074539 6.06813 8.480102 6.999811 +L-Arginine 0.574794 0.200943 1.0 0.144438 1.489464 0 0 0.403393 2.792837 cell 4.234461 5.565819 3.831068 2.772982 4.854714 3.259368 +L-Threonine 0.540842 0.220629 1.0 0.113082 1.454821 0 0 0.316715 2.800767 cell 5.715582 4.30713 3.990415 2.914815 4.961628 3.410472 +L-Glutamine 0.98619 0.263749 1.0 0.087801 1.980946 0 0 0.237703 2.707301 cell 3.806965 2.018081 1.780378 1.099664 2.77178 1.39922 +Glycine 0.567169 0.318145 1.0 -0.012773 1.481613 0 0 -0.035287 2.762706 cell 5.028385 3.20148 3.236767 2.265679 4.012265 2.708039 +Pyruvic_acid 0.472738 0.490805 1.0 -0.131405 1.387741 0 0 -0.317152 2.413541 cell 1.811325 4.224866 2.158282 1.84113 2.766334 1.993409 +L-Alanine 0.440859 0.494601 1.0 -0.237912 1.357412 0 0 -0.631111 2.652708 cell 4.684396 2.511054 3.142165 2.031688 3.42969 2.526638 +Fructose_1,6-bisphosphate 2.638184 1 1 2.0 cell 3.220864 1.220864 3.220864 1.220864 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundance--cell-Control-T2h-Control-T0-Tt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-Control-T2h-Control-T0-Tt.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,25 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_cell_T2h-1 Ctrl_cell_T2h-2 Ctrl_cell_T0-1 Ctrl_cell_T0-2 gmean_1 gmean_2 +L-Tryptophan -0.777998 0.034692 0.69385 0.664552 0.583176 0 0 1.541549 2.319681 cell 2.660282 2.70099 4.242539 4.979963 2.680559 4.596486 +L-Aspartic_acid -2.274085 0.039066 0.781312 0.556683 0.206744 0 0 1.374553 2.469185 cell 0.327076 0.791534 2.796261 2.166087 0.508814 2.461086 +L-Lysine -0.558396 0.071556 1.0 0.497716 0.679057 0 0 1.23415 2.479625 cell 3.776027 3.993588 5.227738 6.255652 3.883284 5.718646 +L-Arginine -0.658636 0.111701 1.0 0.440969 0.633477 0 0 1.087359 2.465839 cell 3.035924 2.953846 4.123283 5.419685 2.994604 4.72725 +L-Histidine -0.68301 0.090057 1.0 0.413676 0.622865 0 0 1.065086 2.574685 cell 2.578187 3.676926 5.152872 4.742012 3.078929 4.943175 +L-Tyrosine -0.589456 0.191484 1.0 0.235832 0.664593 0 0 0.617152 2.616914 cell 2.671781 4.292502 4.909654 5.288695 3.386536 5.095651 +L-Methionine -0.489868 0.261207 1.0 0.168943 0.71209 0 0 0.427099 2.528072 cell 3.0957 4.99071 5.623772 5.417809 3.930616 5.51983 +L-Phenylalanine -0.608451 0.19931 1.0 0.160334 0.655901 0 0 0.442554 2.760207 cell 2.526754 3.990049 4.432603 5.286961 3.175196 4.840971 +L-Malic_acid -0.842519 0.323037 1.0 0.123892 0.557669 0 0 0.2985 2.409353 cell 1.235551 3.317115 3.615615 3.644904 2.024467 3.63023 +Ile_Leu -0.554218 0.227774 1.0 0.111354 0.681026 0 0 0.309498 2.779406 cell 2.749607 4.283823 4.593321 5.529013 3.43203 5.039497 +L-Lactic_acid -0.468969 0.32893 1.0 0.109159 0.722481 0 0 0.264176 2.420103 cell 3.143658 3.203459 3.467635 5.563761 3.173418 4.39239 +Fumaric_acid -1.082458 0.257085 1.0 0.072691 0.472224 0 0 0.201376 2.770286 cell 0.878066 2.539989 2.741365 3.648352 1.493412 3.162509 +L-Glutamine -1.091499 0.265783 1.0 0.064303 0.469274 0 0 0.177439 2.759429 cell 0.883383 1.753625 3.642812 1.931064 1.244638 2.652264 +L-Glutamic_acid -0.765842 0.325511 1.0 -0.028187 0.58811 0 0 -0.078254 2.776208 cell 1.414087 3.21983 4.190295 3.141576 2.133804 3.628241 +L-Valine -0.345997 0.35338 1.0 -0.044413 0.786764 0 0 -0.120212 2.706693 cell 4.179372 6.167004 6.886065 6.046792 5.07683 6.452798 +L-Threonine -0.463814 0.368868 1.0 -0.099423 0.725067 0 0 -0.278707 2.803234 cell 2.723045 4.443183 5.526279 4.164476 3.47836 4.797297 +Pyruvic_acid 0.905946 0.398774 1.0 -0.124124 1.873772 0 0 -0.34081 2.745715 cell 1.633721 3.592255 0.84654 1.974531 2.422549 1.292873 +Hexose-phosphate -0.60704 0.407318 1.0 -0.137592 0.656542 0 0 -0.378236 2.748963 cell 1.734049 3.685036 4.483012 3.3068 2.527851 3.85025 +Hexose -0.403635 0.446592 1.0 -0.201612 0.755951 0 0 -0.558993 2.772623 cell 2.764282 4.423486 5.536905 3.864493 3.496822 4.625725 +L-Serine -0.31232 0.458611 1.0 -0.2056 0.805345 0 0 -0.560471 2.726026 cell 3.868814 5.868893 6.59484 5.308422 4.765045 5.916772 +Fructose_1,6-bisphosphate 0.0 1.526778 0 1 0.0 2.23249 cell 0.154691 2.387181 0.398015 0.60768 0.398015 +Glycine -0.316365 0.624652 -0.423447 0.803091 0 0 -1.102692 2.604084 cell 2.393939 4.284841 4.998023 3.182149 3.202756 3.988039 +L-Proline -0.168249 0.862102 -0.454948 0.889922 0 0 -1.160081 2.549919 cell 2.590021 5.13994 4.720818 3.560737 3.648637 4.09995 +L-Alanine -0.07162 0.950212 -0.89366 0.951569 0 0 -1.882381 2.106373 cell 1.96331 4.069683 4.057263 2.174882 2.826668 2.970533 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-Control-T2h-L-Cycloserine-T2h-Tt.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,25 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_cell_T2h-1 Ctrl_cell_T2h-2 L-Cyc_cell_T2h-1 L-Cyc_cell_T2h-2 gmean_1 gmean_2 +L-Lactic_acid 0.362066 0.35792 1.0 0.058568 1.285265 0 0 0.142099 2.42622 cell 6.256224 6.375234 3.949014 6.114125 6.315449 4.913732 +L-Arginine 0.181307 0.654333 1.0 -0.072802 1.133911 0 0 -0.192713 2.64707 cell 7.128152 6.935439 5.016926 7.663996 7.031135 6.200782 +L-Tryptophan 0.10835 0.575344 1.0 -0.075459 1.077995 0 0 -0.192682 2.553471 cell 12.591879 12.784561 10.562173 13.115644 12.687854 11.769864 +L-Lysine 0.11389 0.744288 1.0 -0.171533 1.082142 0 0 -0.462286 2.695029 cell 8.023523 8.485809 6.395727 9.090756 8.251429 7.62509 +Fumaric_acid 0.29413 0.461999 0 1 0.700935 2.383081 cell 0.888751 2.570897 3.271832 1.511584 3.271832 +Fructose_1,6-bisphosphate 0.0 1.145529 0 1 0.0 2.287469 cell 0.158501 2.44597 0.543545 0.622647 0.543545 +Pyruvic_acid 0.373873 0.661572 -0.465941 1.295827 0 0 -1.181049 2.534762 cell 1.800099 3.958089 1.423327 2.981148 2.669261 2.05989 +L-Glutamine 0.262582 0.678179 -0.482549 1.199624 0 0 -1.200459 2.487743 cell 2.308578 4.582813 2.09507 3.509037 3.252658 2.711398 +L-Aspartic_acid 0.249699 0.745614 -0.577117 1.188959 0 0 -1.388665 2.406211 cell 1.600511 3.873288 1.467077 2.989176 2.489827 2.094123 +Ile_Leu 0.191338 0.775003 -0.624008 1.141823 0 0 -1.493647 2.393636 cell 3.231426 5.034484 2.640848 4.725073 4.033431 3.53245 +L-Phenylalanine 0.185719 0.785147 -0.638734 1.137383 0 0 -1.519477 2.378888 cell 3.147058 4.969585 2.590697 4.666535 3.95469 3.477007 +L-Tyrosine 0.169586 0.805815 -0.669127 1.124736 0 0 -1.570811 2.347552 cell 3.058614 4.91399 2.566438 4.629425 3.876854 3.446902 +L-Valine 0.154185 0.813025 -0.678125 1.112793 0 0 -1.575671 2.32357 cell 3.58809 5.294519 2.970949 5.163761 4.358579 3.916793 +L-Alanine -0.026254 0.973518 -0.688817 0.981966 0 0 -1.603905 2.328493 cell 2.170343 4.498836 2.479673 4.083578 3.124743 3.182128 +L-Histidine 0.111173 0.829889 -0.704841 1.080106 0 0 -1.624902 2.305344 cell 4.258872 6.073864 3.76852 5.883774 5.086041 4.708834 +L-Malic_acid -0.25568 0.834034 -0.711875 0.837592 0 0 -1.640219 2.304084 cell 1.183028 3.176104 1.535885 3.487112 1.938407 2.314261 +Hexose 0.123989 0.851213 -0.738234 1.089743 0 0 -1.678448 2.273598 cell 3.154886 5.048543 2.774945 4.833334 3.990937 3.662272 +Hexose-phosphate 0.02248 0.937522 -0.772684 1.015704 0 0 -1.725995 2.233767 cell 1.985384 4.219151 2.114313 3.840308 2.894242 2.849493 +L-Glutamic_acid 0.071406 0.898587 -0.786571 1.05074 0 0 -1.739625 2.211657 cell 1.73196 3.943617 1.76515 3.504775 2.613463 2.487258 +L-Proline -0.102609 0.921051 -0.798521 0.931347 0 0 -1.759402 2.203325 cell 2.237976 4.441301 2.617836 4.377238 3.152701 3.385098 +L-Threonine 0.069145 0.906001 -0.827452 1.049095 0 0 -1.803085 2.179081 cell 3.176783 5.183546 3.004465 4.979868 4.057955 3.868054 +L-Serine 0.075222 0.909283 -0.832574 1.053523 0 0 -1.804475 2.167344 cell 3.54649 5.379935 3.212591 5.350965 4.368053 4.146138 +L-Methionine 0.080167 0.913957 -0.840739 1.05714 0 0 -1.816896 2.16107 cell 3.053635 4.922895 2.761825 4.870531 3.877206 3.667636 +Glycine -0.003109 0.981504 -0.842581 0.997848 0 0 -1.822182 2.162619 cell 2.737938 4.900557 2.871164 4.693346 3.66298 3.670881 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--cell-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,25 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment L-Cyc_cell_T2h-1 L-Cyc_cell_T2h-2 L-Cyc_cell_T0-1 L-Cyc_cell_T0-2 gmean_1 gmean_2 +L-Aspartic_acid -1.364433 0.130746 0.522986 0.281466 0.388387 0 0 0.763705 2.713309 cell 0.780152 1.589563 3.493461 2.353268 1.113598 2.867237 +Pyruvic_acid 1.004811 0.273062 1.0 0.153419 2.006681 0 0 0.386767 2.520986 cell 1.764929 3.696632 1.378162 1.175646 2.55427 1.272883 +L-Proline 0.453975 0.375728 1.0 -0.027312 1.36981 0 0 -0.070115 2.567204 cell 3.208945 5.365621 3.27906 2.798417 4.149456 3.029221 +L-Alanine 0.395494 0.490938 1.0 -0.247303 1.315393 0 0 -0.66902 2.705267 cell 3.137119 5.166273 3.806139 2.461006 4.025818 3.060544 +L-Glutamine -0.367891 0.54526 -0.322082 0.774915 0 0 -0.864197 2.683155 cell 2.384944 3.994548 5.068099 3.130351 3.086547 3.98308 +L-Arginine -0.26515 0.569639 -0.353864 0.832112 0 0 -0.942768 2.66421 cell 3.571926 5.456573 6.236136 4.513805 4.414802 5.305535 +Ile_Leu -0.052032 0.999845 -0.372715 0.964577 0 0 -0.987815 2.650324 cell 3.358135 6.008459 5.176894 4.189079 4.491906 4.656868 +Glycine 0.253911 0.601429 -0.381709 1.192436 0 0 -0.98425 2.578534 cell 3.495889 5.714551 4.480139 3.136017 4.469613 3.748305 +L-Tyrosine -0.099074 0.925868 -0.397473 0.933632 0 0 -1.041848 2.621181 cell 3.260853 5.882034 5.240632 4.198784 4.379549 4.690872 +L-Valine -0.012332 0.946093 -0.416211 0.991489 0 0 -1.085262 2.607482 cell 3.532767 6.140249 5.271324 4.186062 4.657475 4.697456 +L-Malic_acid -0.310073 0.749772 -0.421482 0.806601 0 0 -1.063593 2.523462 cell 1.986311 4.509773 4.280295 3.216702 2.99296 3.710584 +L-Phenylalanine -0.117435 0.894656 -0.424837 0.921825 0 0 -1.0998 2.588757 cell 3.230833 5.81959 5.2858 4.186 4.336142 4.703866 +Hexose 0.120435 0.752117 -0.433008 1.087063 0 0 -1.088815 2.51454 cell 3.389891 5.904431 4.695803 3.606988 4.473855 4.115544 +L-Lactic_acid -0.064719 0.922245 -0.455322 0.956131 0 0 -1.16852 2.566358 cell 4.680861 7.247219 6.703809 5.535289 5.824365 6.091594 +L-Serine 0.169053 0.680458 -0.460513 1.12432 0 0 -1.121076 2.434406 cell 3.657336 6.091742 4.795994 3.674918 4.720122 4.1982 +L-Methionine -0.005852 0.938944 -0.468109 0.995952 0 0 -1.196896 2.556876 cell 3.348806 5.905682 5.10358 3.906684 4.447132 4.465207 +Hexose-phosphate 0.13795 0.760717 -0.55418 1.10034 0 0 -1.331177 2.402066 cell 2.942487 5.344553 4.330543 2.999366 3.965637 3.604009 +L-Glutamic_acid -0.007244 0.937477 -0.559258 0.994991 0 0 -1.377884 2.46377 cell 2.49992 4.96369 4.295701 2.917817 3.522617 3.540349 +L-Tryptophan -0.049313 0.852261 -0.581752 0.966396 0 0 -1.40667 2.417988 cell 5.818548 7.225218 8.026356 5.608368 6.483847 6.709304 +L-Threonine 0.007882 0.940534 -0.614186 1.005478 0 0 -1.477656 2.405876 cell 3.659188 6.065064 5.482022 4.004366 4.710967 4.685299 +L-Histidine -0.131769 0.796273 -0.655487 0.912712 0 0 -1.55048 2.365386 cell 3.449234 5.385275 5.81462 3.834795 4.309881 4.722063 +L-Lysine 0.027768 0.93853 -0.883894 1.019434 0 0 -1.871833 2.117711 cell 4.914168 6.984898 6.786001 4.867187 5.858751 5.747063 +Fructose_1,6-bisphosphate 3.516217 1 1 2.0 cell 2.794844 0.794844 2.794844 0.794844 +Fumaric_acid 1.574466 1 0 1.289051 cell 5.258464 2.81012 3.969413 5.258464 3.339839 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-Control-T0-L-Cycloserine-T0-Tt.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,20 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_med_T0-1 Ctrl_med_T0-2 L-Cyc_med_T0-1 L-Cyc_med_T0-2 gmean_1 gmean_2 +L-Valine -0.06551 0.004613 0.078425 0.830536 0.955607 0 0 1.806475 2.175072 med 42.7862 42.917067 44.961272 44.723542 42.851584 44.842249 +L-Lactic_acid 0.081287 0.035485 0.603247 0.64986 1.057961 0 0 1.519643 2.338416 med 35.285733 35.209883 33.69024 32.947317 35.247788 33.316708 +L-Arginine 0.006662 0.038909 0.661461 0.622566 1.004628 0 0 1.475052 2.369309 med 417.573697 416.802075 415.204388 415.327023 417.187708 415.265701 +L-Proline -0.114311 0.052379 0.890451 0.495962 0.923823 0 0 1.256673 2.533809 med 22.674872 23.296347 25.208681 24.55302 22.983509 24.878691 +Hexose-phosphate -0.152217 0.121088 1.0 0.441254 0.899867 0 0 1.07635 2.439298 med 15.686678 15.672772 18.11207 16.763028 15.679723 17.424498 +L-Tryptophan 0.139342 0.13131 1.0 0.32956 1.101403 0 0 0.861293 2.613467 med 18.793992 19.207497 17.932699 16.59403 18.99962 17.250384 +L-Phenylalanine -0.070754 0.112054 1.0 0.327323 0.95214 0 0 0.875883 2.675902 med 34.932908 35.642687 37.60881 36.51857 35.286013 37.059681 +L-Methionine -0.05948 0.121063 1.0 0.296729 0.95961 0 0 0.804505 2.711241 med 41.3005 42.222702 44.011741 43.027207 41.759055 43.51669 +L-Alanine -0.186768 0.189622 1.0 0.161521 0.878572 0 0 0.450765 2.790747 med 11.17805 12.28269 13.968797 12.733455 11.71736 13.336831 +Ile_Leu -0.067879 0.266664 1.0 0.038434 0.95404 0 0 0.108567 2.824776 med 29.783216 31.074798 32.607992 31.183365 30.422153 31.887724 +Glycine -0.40224 0.406096 1.0 0.003298 0.756683 0 0 0.00781 2.367806 med 3.275612 3.189559 5.557365 3.283422 3.232299 4.271671 +Pyruvic_acid -0.059155 0.334667 1.0 0.001586 0.959826 0 0 0.004213 2.65712 med 33.153112 31.141204 33.798324 33.157325 32.131415 33.47629 +L-Lysine -0.001834 0.946483 1.0 -0.206473 0.99873 0 0 -0.57111 2.766029 med 90.619429 93.385458 92.395033 91.823923 91.992048 92.109035 +L-Threonine -0.019183 0.467268 1.0 -0.208828 0.986792 0 0 -0.562452 2.693379 med 81.007696 78.916447 81.609826 80.445244 79.955235 81.025443 +L-Asparagine 0.051495 0.479539 1.0 -0.240516 1.036338 0 0 -0.659285 2.74113 med 30.611703 29.072045 29.73133 27.870573 29.831943 28.78592 +Hexose 0.007394 0.632326 1.0 -0.248644 1.005138 0 0 -0.634685 2.552587 med 141.526046 144.078633 142.384333 141.749648 142.796636 142.066636 +L-Serine -0.003785 0.885659 1.0 -0.258807 0.99738 0 0 -0.70402 2.720251 med 82.756733 83.460753 84.697551 81.9773 83.107998 83.326326 +L-Histidine 0.020108 0.536681 -0.307902 1.014035 0 0 -0.82449 2.677766 med 66.478417 67.955877 65.278111 67.302907 67.213087 66.282778 +L-Tyrosine -0.024305 0.567197 -0.345223 0.983294 0 0 -0.912759 2.643971 med 49.917227 51.3987 52.561198 50.485941 50.652548 51.51312 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundance--med-Control-T2h-Control-T0-Tt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-Control-T2h-Control-T0-Tt.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,20 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_med_T2h-1 Ctrl_med_T2h-2 Ctrl_med_T0-1 Ctrl_med_T0-2 gmean_1 gmean_2 +L-Asparagine -0.315743 0.028245 0.508416 0.610328 0.803437 0 0 1.473213 2.413806 med 7.730141 8.16053 10.143947 9.633743 7.942421 9.885554 +L-Phenylalanine -0.084598 0.030111 0.541993 0.671736 0.943047 0 0 1.558881 2.320675 med 32.130034 32.052743 33.688915 34.373418 32.091365 34.029445 +L-Threonine -0.106792 0.033603 0.604856 0.631099 0.928651 0 0 1.495659 2.369928 med 25.045012 25.211552 27.41494 26.707211 25.128144 27.058762 +L-Valine -0.067996 0.042832 0.770972 0.607069 0.953962 0 0 1.446278 2.382394 med 39.306545 40.115539 41.561817 41.688939 39.708982 41.625329 +L-Tyrosine -0.113457 0.046722 0.840993 0.530543 0.924371 0 0 1.321767 2.491346 med 23.066568 23.499488 24.821255 25.557914 23.282022 25.186891 +L-Serine -0.118888 0.05061 0.910985 0.560837 0.920897 0 0 1.364531 2.433027 med 22.588437 21.723711 23.952968 24.156738 22.151855 24.054637 +Hexose-phosphate -0.427357 0.062717 1.0 0.581387 0.743623 0 0 1.378344 2.370787 med 5.030212 6.016094 7.400999 7.394438 5.501112 7.397718 +L-Arginine -0.065823 0.085013 1.0 0.501611 0.9554 0 0 1.222599 2.437347 med 39.86267 38.723983 41.16133 41.085269 39.289202 41.123282 +Hexose -0.087076 0.058805 1.0 0.475511 0.941429 0 0 1.21327 2.551509 med 29.894783 30.658183 31.871453 32.446292 30.274077 32.157588 +L-Histidine -0.096367 0.062761 1.0 0.459013 0.935385 0 0 1.179441 2.569515 med 27.526594 26.774502 28.706035 29.344017 27.147944 29.023273 +Glycine -0.100796 0.063723 1.0 0.454918 0.932518 0 0 1.171006 2.574101 med 26.206344 25.541879 28.11598 27.37735 25.871978 27.744207 +Ile_Leu -0.087322 0.110833 1.0 0.415844 0.941268 0 0 1.04462 2.512048 med 28.487629 28.300899 29.532249 30.812947 28.39411 30.165802 +L-Proline -0.427205 0.130273 1.0 0.377685 0.743701 0 0 0.953724 2.525185 med 5.916471 4.533309 6.870195 7.058494 5.178918 6.963708 +L-Methionine -0.104127 0.121198 1.0 0.325756 0.930368 0 0 0.863734 2.651476 med 22.963857 24.192125 25.055859 25.615333 23.569991 25.334052 +L-Lysine -0.042176 0.194447 1.0 0.300247 0.971189 0 0 0.744058 2.478156 med 54.067768 54.127004 54.871062 56.545924 54.097378 55.702198 +L-Lactic_acid -0.056578 0.275137 1.0 0.176712 0.961542 0 0 0.435423 2.464029 med 37.556173 35.609409 38.073438 37.991596 36.569839 38.032495 +L-Tryptophan -0.176081 0.342876 1.0 0.050641 0.885104 0 0 0.126694 2.501802 med 11.638726 9.52248 11.76542 12.024282 10.527561 11.894147 +L-Alanine -0.072231 0.842985 1.0 -0.299141 0.951166 0 0 -0.800552 2.67617 med 6.849088 9.525258 8.100928 8.90148 8.077087 8.491775 +Pyruvic_acid 0.004852 0.940585 -0.575253 1.003369 0 0 -1.407863 2.447382 med 39.928124 38.520261 40.329053 37.881671 39.217875 39.086211 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundance--med-Control-T2h-L-Cycloserine-T2h-Tt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-Control-T2h-L-Cycloserine-T2h-Tt.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,20 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment Ctrl_med_T2h-1 Ctrl_med_T2h-2 L-Cyc_med_T2h-1 L-Cyc_med_T2h-2 gmean_1 gmean_2 +L-Phenylalanine -0.227241 0.001876 0.035636 0.905036 0.854267 0 0 1.896738 2.09576 med 11.714351 11.686171 13.781931 13.611089 11.700253 13.696244 +L-Tyrosine -0.210967 0.004909 0.093265 0.822767 0.863958 0 0 1.796671 2.183694 med 12.524246 12.759305 14.555976 14.70794 12.641229 14.631761 +Ile_Leu -0.219893 0.005939 0.112833 0.826897 0.858629 0 0 1.799743 2.176503 med 12.110445 12.031063 14.207566 13.910188 12.070689 14.058091 +L-Valine -0.160198 0.012825 0.24368 0.722278 0.894902 0 0 1.65598 2.292719 med 16.643609 16.986162 18.642142 18.936328 16.814013 18.788659 +L-Threonine -0.159992 0.019541 0.371286 0.7134 0.89503 0 0 1.632915 2.28892 med 16.648332 16.759038 18.937252 18.391953 16.703593 18.662611 +L-Proline -0.98264 0.022874 0.434602 0.658092 0.506053 0 0 1.551275 2.35723 med 2.305637 1.766621 3.856912 4.123851 2.018214 3.988149 +Hexose -0.2207 0.024599 0.467389 0.64383 0.858149 0 0 1.52812 2.373482 med 11.643072 11.940391 14.016554 13.468511 11.790794 13.7398 +Glycine -0.173877 0.028221 0.536206 0.613466 0.886457 0 0 1.477944 2.409171 med 15.362891 14.973364 16.840835 17.382535 15.166877 17.109541 +L-Serine -0.217541 0.030833 0.585825 0.595079 0.86003 0 0 1.446276 2.430393 med 12.143564 11.678687 13.58984 14.10908 11.908857 13.847026 +L-Histidine -0.137109 0.034656 0.658468 0.574503 0.909339 0 0 1.408935 2.45244 med 19.638732 19.102155 21.047667 21.554595 19.368585 21.299623 +L-Methionine -0.207039 0.045452 0.863579 0.525451 0.866313 0 0 1.3152 2.502993 med 12.063407 12.708642 14.023842 14.5664 12.381822 14.292547 +L-Lysine -0.025559 0.104493 1.0 0.448561 0.98244 0 0 1.10921 2.472817 med 100.041785 100.151388 102.514602 101.260598 100.096571 101.885671 +Hexose-phosphate -0.359685 0.092784 1.0 0.440559 0.779335 0 0 1.109796 2.519066 med 5.940748 7.105089 8.214885 8.459814 6.496887 8.33645 +L-Asparagine -0.341921 0.124809 1.0 0.353378 0.78899 0 0 0.914077 2.586687 med 6.281405 6.631133 7.54521 8.868092 6.453901 8.179952 +L-Lactic_acid -0.10481 0.179465 1.0 0.178872 0.929927 0 0 0.498003 2.784136 med 22.37888 21.218847 22.876883 24.002983 21.791146 23.43317 +L-Arginine -0.030855 0.279162 1.0 0.132376 0.97884 0 0 0.337068 2.546283 med 67.988605 66.046493 68.325673 68.592776 67.010514 68.459094 +L-Alanine -0.443451 0.222838 1.0 0.113513 0.735373 0 0 0.3169 2.79175 med 3.755311 5.222638 5.539538 6.547061 4.428615 6.022266 +Pyruvic_acid -0.070842 0.413764 1.0 -0.116088 0.952082 0 0 -0.307971 2.652915 med 23.31152 22.489558 23.003549 25.142473 22.896851 24.049243 +L-Tryptophan 0.004678 0.946377 1.0 -0.26993 1.003247 0 0 -0.736036 2.726765 med 14.996403 12.269638 13.157757 13.893793 13.564676 13.520767 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundance--med-L-Cycloserine-T2h-L-Cycloserine-T0-Tt.tsv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,20 @@ +metabolite log2FC pvalue padj distance/span FC count_nan_samples_group1 count_nan_samples_group2 distance span_allsamples compartment L-Cyc_med_T2h-1 L-Cyc_med_T2h-2 L-Cyc_med_T0-1 L-Cyc_med_T0-2 gmean_1 gmean_2 +L-Arginine -0.028306 0.009613 0.163421 0.808209 0.980571 0 0 1.770679 2.190869 med 99.783635 100.173715 101.944394 101.974504 99.978485 101.959448 +L-Proline 0.441124 0.016987 0.288782 0.718846 1.357661 0 0 1.64444 2.287611 med 7.203777 7.702354 5.559337 5.414743 7.448895 5.486564 +Hexose 0.141018 0.04318 0.734054 0.618875 1.102683 0 0 1.46312 2.364161 med 20.919801 20.101843 18.638723 18.55564 20.506744 18.597135 +Hexose-phosphate -0.21989 0.073263 1.0 0.469101 0.858631 0 0 1.183673 2.523277 med 11.042011 11.371231 13.565288 12.554904 11.205412 13.050321 +L-Lactic_acid 0.129519 0.080906 1.0 0.431162 1.093929 0 0 1.107572 2.568806 med 20.843746 21.869766 19.736174 19.30096 21.350594 19.517354 +L-Phenylalanine 0.071888 0.086895 1.0 0.411507 1.051091 0 0 1.064817 2.587604 med 37.870329 37.400886 36.336069 35.282725 37.634876 35.805524 +L-Tyrosine 0.073205 0.130892 1.0 0.338927 1.052051 0 0 0.880001 2.596432 med 35.077787 35.443998 34.197786 32.847566 35.260417 33.515877 +L-Serine 0.094869 0.119025 1.0 0.303502 1.067968 0 0 0.820491 2.703409 med 27.149162 28.186476 26.328671 25.483067 27.662957 25.902419 +L-Valine 0.026692 0.156019 1.0 0.275356 1.018673 0 0 0.72888 2.647043 med 91.228609 92.66826 90.499729 90.021217 91.945617 90.260156 +L-Histidine 0.06085 0.160307 1.0 0.217054 1.04308 0 0 0.599017 2.759755 med 40.2211 41.189815 38.43006 39.622083 40.702576 39.02152 +L-Lysine -0.018451 0.203814 1.0 0.160847 0.987293 0 0 0.441277 2.743465 med 124.61713 123.092758 125.836223 125.058407 123.852599 125.446712 +Ile_Leu 0.064692 0.208392 1.0 0.155183 1.045861 0 0 0.425368 2.741066 med 36.641515 35.874575 35.449207 33.900449 36.256017 34.66618 +L-Threonine 0.034018 0.28585 1.0 0.039028 1.02386 0 0 0.107299 2.749299 med 61.975824 60.191229 60.08393 59.226525 61.077009 59.653687 +L-Methionine 0.043433 0.307379 1.0 -0.00305 1.030563 0 0 -0.008477 2.778959 med 45.649117 47.415202 45.657594 44.636243 46.52378 45.14403 +L-Alanine 0.184452 0.318436 1.0 -0.007446 1.136385 0 0 -0.020451 2.746709 med 10.230133 12.090774 10.250584 9.344065 11.121611 9.786834 +Glycine -0.329159 0.464864 1.0 -0.047343 0.796 0 0 -0.112992 2.386685 med 3.512786 3.625778 5.832897 3.446212 3.568835 4.483458 +Pyruvic_acid 0.016539 0.811502 1.0 -0.212837 1.01153 0 0 -0.57825 2.716869 med 29.219182 31.936051 30.489745 29.911495 30.547427 30.199236 +L-Asparagine 0.077673 0.588663 -0.337812 1.055314 0 0 -0.839365 2.484712 med 13.751007 16.161935 14.590372 13.677223 14.907813 14.126421 +L-Tryptophan -0.041416 0.603384 -0.389154 0.971701 0 0 -1.010695 2.597159 med 26.14293 27.605347 28.740089 26.594652 26.864189 27.646567 |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/abundances--T0--cell--label-n_pc.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--T0--cell--label-n_pc.svg Tue Oct 10 11:52:44 2023 +0000 |
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| @@ -0,0 +1,5 @@ +Explained Variance % PC +88.060744 PC1 +8.81805 PC2 +3.121206 PC3 +0.0 PC4 |
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| diff -r 000000000000 -r c46d33411495 test-data/abundances--cell_pc.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--cell_pc.csv Tue Oct 10 11:52:44 2023 +0000 |
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| @@ -0,0 +1,9 @@ +PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 name_to_plot condition timepoint timenum compartment original_name +6.08216 -0.21243 2.741629 -0.415911 -0.034854 -0.297123 0.029912 0.0 Ctrl_cell_T0-1 Control T0 0 cell MCF001089_TD01 +4.441447 -3.400088 -2.014018 -0.157591 -0.036533 0.034759 0.178162 0.0 Ctrl_cell_T0-2 Control T0 0 cell MCF001089_TD02 +-4.500212 -0.722539 -0.451432 -1.053058 0.388746 -0.337473 -0.380903 0.0 Ctrl_cell_T2h-1 Control T2h 2 cell MCF001089_TD07 +2.559191 3.507152 -1.423484 -0.413442 -0.773312 0.004868 -0.038496 0.0 Ctrl_cell_T2h-2 Control T2h 2 cell MCF001089_TD08 +-0.401209 -0.824396 0.821053 0.46477 -0.229954 0.808554 -0.295096 0.0 L-Cyc_cell_T0-1 L-Cycloserine T0 0 cell MCF001089_TD19 +-4.205021 -0.692778 0.222305 1.352186 -0.581771 -0.490783 0.027384 0.0 L-Cyc_cell_T0-2 L-Cycloserine T0 0 cell MCF001089_TD20 +-5.80631 0.441183 0.660591 -0.656464 0.098959 0.278277 0.454242 0.0 L-Cyc_cell_T2h-1 L-Cycloserine T2h 2 cell MCF001089_TD25 +1.829954 1.903895 -0.556645 0.87951 1.16872 -0.001079 0.024794 0.0 L-Cyc_cell_T2h-2 L-Cycloserine T2h 2 cell MCF001089_TD26 |
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| diff -r 000000000000 -r c46d33411495 test-data/abundances--cell_var.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--cell_var.csv Tue Oct 10 11:52:44 2023 +0000 |
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| diff -r 000000000000 -r c46d33411495 test-data/abundances--med_pc.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--med_pc.csv Tue Oct 10 11:52:44 2023 +0000 |
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| diff -r 000000000000 -r c46d33411495 test-data/abundances--med_var.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/abundances--med_var.csv Tue Oct 10 11:52:44 2023 +0000 |
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| diff -r 000000000000 -r c46d33411495 test-data/example1_metadata.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example1_metadata.csv Tue Oct 10 11:52:44 2023 +0000 |
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| diff -r 000000000000 -r c46d33411495 test-data/example2_metadata.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example2_metadata.csv Tue Oct 10 11:52:44 2023 +0000 |
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| @@ -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 000000000000 -r c46d33411495 test-data/example3_metadata.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/example3_metadata.csv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,19 @@ +name_to_plot condition timepoint timenum compartment original_name +Ctrl_cell_T0h-1 Control T0h 0 cell Sample1 +Ctrl_cell_T0h-2 Control T0h 0 cell Sample2 +Ctrl_cell_T0h-3 Control T0h 0 cell Sample3 +Ctrl_cell_T2h-1 Control T2h 2 cell Sample4 +Ctrl_cell_T2h-2 Control T2h 2 cell Sample5 +Ctrl_cell_T2h-3 Control T2h 2 cell Sample6 +Cond1_cell_T0h-1 Cond1 T0h 0 cell Sample7 +Cond1_cell_T0h-2 Cond1 T0h 0 cell Sample8 +Cond1_cell_T0h-3 Cond1 T0h 0 cell Sample9 +Cond1_cell_T2h-1 Cond1 T2h 2 cell Sample10 +Cond1_cell_T2h-2 Cond1 T2h 2 cell Sample11 +Cond1_cell_T2h-3 Cond1 T2h 2 cell Sample12 +Cond2_cell_T0h-1 Cond2 T0h 0 cell Sample13 +Cond2_cell_T0h-2 Cond2 T0h 0 cell Sample14 +Cond2_cell_T0h-3 Cond2 T0h 0 cell Sample15 +Cond2_cell_T2h-1 Cond2 T2h 2 cell Sample16 +Cond2_cell_T2h-2 Cond2 T2h 2 cell Sample17 +Cond2_cell_T2h-3 Cond2 T2h 2 cell Sample18 \ No newline at end of file |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/legend-abundances-cell.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/legend-abundances-cell.svg Tue Oct 10 11:52:44 2023 +0000 |
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| diff -r 000000000000 -r c46d33411495 test-data/legend.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/legend.svg Tue Oct 10 11:52:44 2023 +0000 |
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| diff -r 000000000000 -r c46d33411495 test-data/legend_isotopologues_stackedbars.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/legend_isotopologues_stackedbars.svg Tue Oct 10 11:52:44 2023 +0000 |
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| b |
| diff -r 000000000000 -r c46d33411495 test-data/pathways_kegg_metabolites.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathways_kegg_metabolites.csv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,8 @@ +"CENTRAL_CARBON_METABOLISM" "AMINOACIDS" +"Fumaric_acid" "L-Glutamine" +"Citric_acid" "L-Asparagine" +"Hexose" "L-Aspartic_acid" +"L-Lactic_acid" "L-Glutamic_acid" +"Pyruvic_acid" "L-Glutamine" +"Hexose-phosphate" "L-Proline" + "L-Alanine" |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/pathways_kegg_transcripts.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pathways_kegg_transcripts.csv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,12 @@ +"CENTRAL_CARBON_METABOLISM" "AMINOACIDS" +"ALDOA" "ADSS1" +"GPI" "AGXT" +"PCK1" "ASL" +"PGAM1" "ASNS" +"PKM" "ASPA" +"IDH1" "GAD1" +"MDH2" "GLS" +"PC" "GLUD1" +"SDHA" "GLUD2" +"SUCLG1" +"SUCLG2" |
| b |
| diff -r 000000000000 -r c46d33411495 test-data/rawAbundances.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rawAbundances.csv Tue Oct 10 11:52:44 2023 +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 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| b |
| diff -r 000000000000 -r c46d33411495 test-data/rawAbundances3.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rawAbundances3.csv Tue Oct 10 11:52:44 2023 +0000 |
| b |
| @@ -0,0 +1,7 @@ +ID Sample1 Sample2 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 +Fumaric_acid +Glycine 31339.848144444444 39953.502358333335 25011.070372222222 1867.879408333334 2173.435886666666 1221.041376190477 115741.494772222224 125731.819858333336 182398.016666666 560.116666667 19650482.416666664 656.516666666 35768152.41666667 21132662.81666667 21540901.71666667 22233782.916666664 26243782.873465 26439782.65765756 +Hexose 15263.525582222223 10653.204421666667 17620.2662477777785 2194.176071666667 3284.639177333334 2131.811518095239 6702.562494444444 6744.364736666666 5678.643333334 24242428.643333334 22336054.643333334 22906432.643333334 23957348.643333334 23850557.643333334 26889340.643333334 25837975.643333334 31838775.948787 29134981.16455938 +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-Glutamine 8606.32958888889 9863.261441666667 9512.041427777778 18956.960391666667 18701.497033333335 15374.547080952381 4094.7460777777783 4858.299791666668 +L-Tryptophan 4101.068422222223 4813.902566666667 4571.5729777777774 2610.923316666667 2975.5369333333333 2079.1386666666667 32157.056777777778 32678.538611666667 293656601.733333334 24177093.733333334 23401859.733333334 19146747.733333334 22572464.733333334 20887438.733333334 20532655.733333334 21681238.733333334 19681235.1976875 21681931.65426354 \ No newline at end of file |
