2 Commits

Include renames

Author	SHA1	Message	Date
kemalandClaude Opus 5.5	9149ef328a	Apply the brand across the repo: reports, README, guide ... * simurg/core/brand.py: single source of the mark geometry, colours, favicon and the report header band (scripts/brand now load it from there). * HTML reports (QC report, compare dashboard, methylation QC): offline SVG favicon, indigo header band with the mark, version and a sha256 of the data shown; Noto Sans font stack; methylation plots in Okabe-Ito colours. * README banner, guide logo, brand/blog links; branding brief updated to the final identity; Noto (OFL) and Okabe-Ito entries in THIRD_PARTY_NOTICES; CHANGELOG (Unreleased). Unit tests + P5 QC oracle: 285 passed; ruff and mypy clean. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-30 08:01:30 +01:00
kemalandClaude Opus 5.5	c1c2c30c87	v2 methylation control QC (WIP): simurg methyl qc|convert-manifest (MET-001..018) ... Methylation CSV manifest reader (MET-002/003), raw M/U assembly with bead masking (MET-005), pOOBAH detection p-values, noob background correction, linear/nonlinear dye bias, beta and M-values (MET-010..012), the 21 methylation control metrics (MET-006, bs-conv red-bg set option), per-sample ctrl/cgs tables, summary tsv/xlsx/html with the detection histogram and a beta PCA, pcs.tsv.gz, controls_raw/controls_qc.tsv; methylation datasets load in qc report (MET-014); qc controls --array-type methylation; minfi-style Sentrix_ID/Sentrix_Position sheet keys. Vendor EPIC manifests carry a 5th field on some control lines: >= 4 fields accepted. Runs on the public minfiDataEPIC set (3 x NA12878). Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv	2026-09-29 00:13:22 +01:00