First commit; adding README
Initial commit of hotnet2 and runHotnet2 modules
Adds example configurations for directed and classic examples.
Similarity matrix calculation for hotnet now ensures that influence matrix is symmetric
Updates sample configs to use heat file accessible to compbio group
Adding Max's delta.py
Non-parallelized version of delta-finding procedure implemented.
Parallelized version of delta-finding procedure impelemented
Updates network delta selection to use common code paths regardless of whether run in parallel
Updates arg file parser in findThreshold.py (Need to factor this out at some point)
Adding Max's stats.py
runHotnet2.py now produces JSON output
Includes parameters in runHotnet2.py output
runStats matches runHotnet2
runStats.py now working
Significance testing cleanup
findThreshold.py can now be used for heat permutation delta-finding procedure (non-multithreaded only)
findThreshold.py heat permutation delta-finding procedure now works multithreaded; multi/non-multi share common code path
Removes commented out test code from findThreshold.py
Removes old sample config