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v1.2.11

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@jab57 jab57 released this 03 Oct 23:20
· 25 commits to main since this release
v1.2.11
9525002

TCGA networks are no longer bundled

The 14 TCGA tumor-state ARACNe networks come from the Bioconductor package aracne.networks (F. M. Giorgi), which is distributed under a Columbia University software evaluation license (non-commercial academic research use only; no redistribution — full license). RegNetAgents therefore no longer includes them. Install them from Bioconductor:

pip install -e ".[tcga]"
python scripts/setup_tcga_networks.py --accept-license

The setup script checks every network against a recorded checksum, so installed networks are identical to those shipped in v1.2.10 and earlier. Everything else — the GREmLN cell-type networks and IntOGen driver annotation — works without them.

Other changes

  • Corrected the attribution of aracne.networks (Federico M. Giorgi) and removed an invalid DOI from the documentation.
  • verify_installation.py: the TCGA networks are an optional check, Git LFS is no longer needed to run the tool, and two fixes (a summary bug that could hide a failed required check; a crash on Windows consoles).
  • aracne.networks download URLs pinned to Bioconductor 3.23/3.22.

Licensing

The MIT license covers the RegNetAgents source code. Data obtained through the setup scripts remain under their upstream licenses.

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