Chapter 9 Network inference

SJARACNe is a scalable software tool for gene network reverse engineering from big data. As an improved implementation of the ARACNe, SJARACNe achieves a dramatic improvement in computational performance in both time and memory usage and implements new features while preserving the network inference accuracy of the original algorithm.

Similar to MICA, SJARACNe is also a component of scMINER framework, and can work seamlessly with the SparseExpressionSet object. The input for MICA can be easily generated from the SparseExpressionSet object by generateSJARACNeInput(), and the output of SJARACNe, the networks, can be effortlessly assessed by drawNetworkQC() and directly taken for driver activity estimation by getActivity_individual() and getActivity_inBatch().