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README.rst

DiffSLc

To use DiffSLc's python implementaiton, simply import it as package:

>>> from diffslcpy import diffslc
>>> print diffslc.DiffSLc

Or use the command line tool:

$ diffslcpy-cl --help
Usage: diffslcpy-cl [options] arg

Options:
-h, --help            show this help message and exit
-c COEXPRFILE, --coexpr_file=COEXPRFILE
                      File containing the gene coexpression matrix.
                      [coexpression.expr]
-g NETFILE, --graph_file=NETFILE
                      File containing the PPI network in NetworkX adjacency
                        list or GraphML format. [graph.graphml]

--

Additional instructions:

  • The coexpression matrix is optional if the edges in the graph already have coexpr attribute that holds the coexpression value.
  • If both, a coexpression matrix and a network file, are provided, the values in coexpression matrix will overwrite the coexpr edge attribute of the network.
  • If both, a coexpression matrix and a network file, are provided, the mapping between network nodes and corresponding row/column names in the coexpression matrix must be the same. DiffSLc will look for coexpression values in the coexpression matrix based on the network node names.
  • If you do not have a mapping between your graph nodes and the data you used to create coexpression matrix, there is detailed information provided in the diffslc repository README's section 3a and 3b (and the associated source code mentioned therein).

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DiffSLc implementation in Python (Work In Progress)

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