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bio-copy-number-recurrent-cnv

Identify recurrent and driver copy number alterations across a tumor cohort with GISTIC2 (G-score, Ziggurat deconstruction, focal vs broad/arm-level analysis, q-values from permutation) and quantify copy-number signatures with the Steele 2022 COSMIC framework and the Drews 2022 CINSignatures framework. Covers driver-gene localization from recurrence peaks, distinguishing focal drivers from arm-lev

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Version Compatibility

Reference examples tested with: GISTIC 2.0.23, R 4.3+ with CINSignatureQuantification 1.2+; Python 3.10+ with SigProfilerAssignment 0.1+ (optional, COSMIC CN signatures).

Before using code patterns, verify installed versions match. If versions differ:

  • CLI: gistic2 --help (GISTIC 2.0 is a MATLAB-compiled binary; needs the MCR runtime)
  • R: packageVersion('CINSignatureQuantification')
  • Python: pip show SigProfilerAssignment

GISTIC 2.0 has had no substantive rel

[Description truncada. Veja o README completo no GitHub.]

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