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Small updates authored by Thomas Van Parys's avatar Thomas Van Parys
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......@@ -8,7 +8,7 @@ ModuleViewer is a tool to directly generate annotated heat maps from gene cluste
Creation of images relies on at least two types of data: the data matrix and the modules file. Optionally, this can be extended with regulator data, a condition tree, and annotation files.
* **data matrix**: The expression data. The header contains the name of all experiments (conditions), the first column represents gene names. The rest of the data consists of the expression data.
* **data matrix**: This TAB-delimited file describes the expression data. The header contains the name of all experiments (conditions), the first column represents gene names. The second column can be left empty, or be used for symbolic gene names. The rest of the data consists of the expression data.
* **gene file**: Either an [XML file](TreeFile) with modules and genes, possibly grouped together into a tree structure, or a [simple list](ListFile) of modules with their genes.
* **condition tree**: (optional) By default, each module displays all conditions, in the same order as given in the expression matrix. A more fine grained representation can be defined using an [XML file](TreeFile). This file specifies conditions to be displayed per module, possibly grouped together into a tree structure.
* **regulator tree**: (optional) [XML file](TreeFile) with regulator genes or a [simple list](ListFile) of regulators assigned to modules.
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