Table 1.
Description of the programs available in NeAT
| Program | Description | Input | Output |
|---|---|---|---|
| Network tools | |||
| convert-graph | Converts a graph from a format to another one, position the nodes and changes the edge colors and width according to its weight | A network in a given format | A network in the requested format |
| display-graph | Draws a network graphical representation | A network | A figure in the requested format |
| compare-graphs | Computes the intersection, the union or the difference of two networks | Two networks to be compared | A network (intersection, union, difference) |
| random-graph | Generates random graphs either from an existing graph or from scratch according to different randomization procedure. | A graph or a list of node names or nothing | A randomized network |
| graph-topology | Calculates the degree, betweenness and closeness of each node and specifies if this node is a source or a target node | A network, (list of nodes for which the degree has to be computed) | A table the requested centrality statistics of each requested node |
| alter-graph | Alters a graph either by adding or removing edges or nodes (targeted removal or not) | A network | An altered network |
| Pathfinder | Finds the k-shortest path between a set of source nodes and a set of target nodes | A network and the list of source and target nodes | A table of pathway or a network composed of the set of pathways |
| String dataset download | Downloads a subset of the network of the String database (40) | A list of nodes for which you want to know the neighbors in String | The neighbors of the nodes your entered in and the edges between them. |
| Network clusters tools | |||
| MCL (34,36) and RNSC (37) | Finds the densely connected subsets of the graph | A network | A list of clusters |
| graph-cligue | Extract al cliques from a graph | A network | A list of cliques |
| graph-neighbours | Extracts from a graph the neighborhood of a set of seed nodes | A network, (a list of seed nodes) | Clusters of neighbor-source node pairs |
| graph-cluster-membership | Maps a clustering result onto a graph and compute the membership degree between each node and each cluster, on the basis of edges linking this node to the cluster | A network, clustering results | A tab-delimited membership table, where each row represents a node and each column a cluster. Entries are the membership degree of the node. |
| graph-get-clusters | Compares a graphs with clusters. Extracts the intra-clusters edges or map the clusters on the network | A network | An edge-labeled network |
| Clusters tools | |||
| compare-classes | Compares two class files (the query file and the reference file). Each class of the query file is compared to each class of the reference file. | One or two cluster files | For each comparison, the number of common elements and comparison statistics or a contingency table |
| contingency-stats | Study of a contingency table | A contingency table | Statistics according to ref. (26) |
| Others tools | |||
| roc-stats | Calculates and draws ROC curve | Scored results associated with validation labels | For each score value, the derived statistics (Sn, PPV, FPR), which can be further used to draw a ROC curve. |
Input Parameters between brackets are optional.