0.7.2

• PANDA reads arguments as dataframes in addition to file paths
• changed condor ground truth to match output of python-igraph 0.8.2.

0.7.1

• Major fix for OTTER behavior across platforms.

0.7

• new tool: OTTER
• unit test for OTTER
• fix for PANDA force field
• tweaks for compatibility of gpuPANDA with cupy

Stockholm

• Added gpuPANDA, which is a gpu-accelerated implementation of PANDA
• Added gpuLIONESS
• Added a gpuPANDA and gpuLIONESS tutorial
• Fixed condor dependency to python-igraph (still under investigation in #82 )

0.6.1

• Created three options for data processing in PANDA.

  • Union: adds rows for genes/TFs that are missing in at least one prior (expression, ppi, motif)
  • Intersection: removes TF/genes that missing in at least one prior
  • Legacy: previous data processing behavior

• The default was set to union in netZooM, netZooR, netZooPy as it is the default in netZooC.

SAMBAR

• pysambar was added
• LIONESS tutorial was added

CONDOR

• we added CONDOR to netZooPy.

PUMA

• pypuma was added to netZooPy.

LIONESS

• LIONESS was added

original import

• This is the original code as imported from Alessandro, Marieke, and Tian Wang repos.
• PANDA was added.