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Untrack nested repos atlas and external/MutSig2CV_src CI #370: Commit 5a2f08c pushed by ahmed-shuaibi
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Consolidate docs into AGENTS.md; add .grok agent config CI #369: Commit 431f493 pushed by ahmed-shuaibi
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EM: random restarts (n_inits=10) to guard against local optima (R3-5) CI #368: Commit ba71dac pushed by ahmed-shuaibi
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Regenerate Table S5 (R1 columns): symmetric FDR<0.01, per-BMR ME/CO, … CI #367: Commit 442e1d9 pushed by ahmed-shuaibi
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Regenerate Table S5 (R1 columns): symmetric FDR<0.01, per-BMR ME/CO, … CI #366: Commit 6ea5be2 pushed by ahmed-shuaibi
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Add BMR-calibration + subtype-split analyses (rebuttal corroboration) CI #365: Commit f10cc4c pushed by ahmed-shuaibi
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Add BMR-calibration + subtype-split analyses (rebuttal corroboration) CI #364: Commit ca2c14f pushed by ahmed-shuaibi
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atlas exporter: add per-cohort cBioPortal study links (TCGA) CI #363: Commit 36467c1 pushed by ahmed-shuaibi
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Add atlas data exporter (CSV -> atlas.json for the DIALECT Atlas site) CI #362: Commit c2c821c pushed by ahmed-shuaibi
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Graph Update: pip in /. #1416791653 Dependency Graph #3: by dependabot Bot
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Add rebuttal analysis scripts (network extraction, over-correction, f… CI #361: Commit 93b6902 pushed by ahmed-shuaibi
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style: shorten docstring usage example (ruff clean) CI #360: Commit 4c90672 pushed by ahmed-shuaibi
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style: import matplotlib as mpl + wrap legend labels (ruff clean) CI #359: Commit 88640c3 pushed by ahmed-shuaibi
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analysis: per-cohort ME/CO interaction network plots (bold nodes, thi… CI #358: Commit 3a34df4 pushed by ahmed-shuaibi
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fix: set-u-safe empty cb_arg expansion (cohorts without q_values.txt) CI #357: Commit 20403a1 pushed by ahmed-shuaibi
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fix: guard tau-EM against degenerate pairs (fall back to independence) CI #356: Commit 4be6974 pushed by ahmed-shuaibi
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style: drop unused root arg from load_passengers CI #355: Commit a082c8e pushed by ahmed-shuaibi
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fix: resolve likely-passenger path from repo data/ regardless of resu… CI #354: Commit 0fea157 pushed by ahmed-shuaibi
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feat: master run-everything driver (all TCGA + all MSK, all 3 BMRs) CI #353: Commit 0253102 pushed by ahmed-shuaibi
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feat: orchestrator MutSig stage uses Octave-patched source + proper l… CI #352: Commit c843edf pushed by ahmed-shuaibi
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analysis: DIALECT extractor for the proper MutSig per-sample lambda BMR CI #351: Commit 0f0f818 pushed by ahmed-shuaibi
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feat: extract proper per-sample BMR from patched MutSig2CV via Octave CI #350: Commit 458eb00 pushed by ahmed-shuaibi
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fix: match browser duplicate-named tarballs (study (1).tar.gz) in Dow… CI #349: Commit 3e1b10b pushed by ahmed-shuaibi
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scripts: MSK per-cancer-type stratification + driver; parameterize or… CI #348: Commit c30e443 pushed by ahmed-shuaibi
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fix: redirect per-cohort verbose output to output/pancan/<C>/pipeline… CI #347: Commit 4ca3fd4 pushed by ahmed-shuaibi
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