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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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scripts: two-pass pancan driver + reorder pipeline (CBaSE/DIG before … CI #346: Commit 6ee785f pushed by ahmed-shuaibi
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fix: DIG stage writes bmr_pmfs.dig.csv directly to the cohort dir CI #345: Commit cc9272a pushed by ahmed-shuaibi
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style: drop now-redundant noqa directives (scripts/* ignores S603/S607) CI #344: Commit fda6717 pushed by ahmed-shuaibi
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scripts: idempotent per-cohort pipeline runner + download retry/backoff CI #343: Commit aac50ee pushed by ahmed-shuaibi
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Graph Update: pip in /. #1411217059 Dependency Graph #2: by dependabot Bot
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scripts: cBioPortal PanCancer MAF fetcher (tarball or datahub) CI #342: Commit f14ddc6 pushed by ahmed-shuaibi
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style: wrap final long line in bmr_passenger_proportions docstring CI #341: Commit cd77873 pushed by ahmed-shuaibi
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analysis: paper-faithful likely-passenger proportions per BMR CI #340: Commit 1da7204 pushed by ahmed-shuaibi
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Graph Update: pip in /. #1411204289 Dependency Graph #1: by dependabot Bot
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docs: fix README Python API + CLI to match the current surface CI #339: Commit 32b2e6f pushed by ahmed-shuaibi
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