Mercurial > repos > bimib > cobraxy

comparison COBRAxy/flux_to_map.xml @ 165:2be342a25cdb draft

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Uploaded
author luca_milaz
date Mon, 18 Nov 2024 17:20:03 +0000
parents 0a043d85070e
children a057458bfa4e
comparison
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164:929104dceba8 165:2be342a25cdb
154 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example. 154 - custom svg map. Graphical elements must have the same IDs of reactions. See HmrCore svg map for an example.
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156 The tool generates: 156 The tool generates:
157 - 1) a tab-separated file: reporting fold-change and p-values of fluxes between a pair of conditions/classes; 157 - 1) a tab-separated file: reporting fold-change and p-values of fluxes between a pair of conditions/classes;
158 - 2) a metabolic map file (downloadable as .svg and .png): visualizing up- and down-regulated reactions between a pair of conditions/classes; 158 - 2) a metabolic map file (downloadable as .svg and .png): visualizing up- and down-regulated reactions between a pair of conditions/classes;
159 - 3) two metabolic maps to visualize the mean and median fluxes normalized amongst all classes. The associated color map is also generated. 159 - 3) two metabolic maps to visualize the mean and median fluxes normalized amongst all classes. The associated color map is also generated;
160 - 4) a log file (.txt). 160 - 4) a log file (.txt).
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162 Output options: 162 Output options:
163 To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’). 163 - To calculate P-Values and Fold-Changes and to enrich maps, comparisons are performed for each possible pair of groups (default option ‘One vs One’).
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165 Alternative options are: 165 Alternative options are:
166 - comparison of each group vs. the rest of samples (option ‘One vs Rest’) 166 - comparison of each group vs. the rest of samples (option ‘One vs Rest’)
167 - comparison of each group vs. a control group (option ‘One vs Control). If this option is selected the user must indicate the control group label. 167 - comparison of each group vs. a control group (option ‘One vs Control). If this option is selected the user must indicate the control group label.
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