llms.txt
+8
https://cybergenic.im/llms.txt
+ - [Checking the scan against SelectSim (research note)](https://cybergenic.im/blog/co-mutation-scan-vs-selectsim): The scan's published snapshot compared pair by pair with SelectSim (Iyer et al., Nature Genetics 2026), from both methods' public files: where both call a gene pair they give it the same direction in 159 of 161 on largely shared MSK patients; SelectSim calls about 7 times as many pairs (the methods differ in their null, in which tumours they count and in which mutations); and a dire+ - [BRAF, KRAS, EGFR mutual exclusivity by tumour type (research note)](https://cybergenic.im/blog/braf-kras-egfr-exclusivity-within-tumour-types): A re-test of Vaeyens et al. (Int J Cancer 2026): its 10,956 variant-level co-mutation tables rebuilt from the authors' published patient file, every significant call re-tested within tumour types and against chance (the study's variant-pair test counts only tumours with either gene mutated, which inflates exclusivity), then its variant classes tested + ## Data+ - [Open co-alteration dataset](https://cybergenic.im/data): Every gene pair the discovery scan tested in 50 tumour cohorts, significant or not, as one Parquet file (195,095 rows): 2x2 counts, the burden-conditional expected count, p and Benjamini-Hochberg q values, the effect of record and the scan's gate outcomes, with SHA-256 checksums. CC BY-NC 4.0. Also on Hugging Face as cybergenic/cancer-mutation-co-occurrence (load_dataset), DOI 10.57967/hf/10761.+ - [Gene pair pages](https://cybergenic.im/pairs): One page per gene pair the scan keeps in at least one cohort, listed here and in the sitemap; each shows the pair in every cohort that tested it (tumours, tumours with both mutations, the expected count under the burden-conditional null and under independence, odds ratio, q, the direction where the data establish one, and the scan's gate outcome). Any tested pair answers at /pairs/<gene>-and-<gene> in lower case, for example /pairs/kras-and-stk11+ - [SelectSim comparison files](https://cybergenic.im/data/external-agreement/selectsim-2026-10-03/README.md): Every gene pair either method calls in a tumour type both tested, with both methods' statistics (comparison.csv, 2,449 rows), every tally of the comparison (summary.json), the code that made them, and SHA-256 checksums.+ - [BRAF, KRAS and EGFR re-test files](https://cybergenic.im/data/external-agreement/vaeyens-2026-braf-kras-egfr/README.md): The re-test of Vaeyens et al.: a script that rebuilds every one of the study's tables from its authors' repository and re-tests each within tumour types, in the study's design and against chance, every test with its statistics, the cohort class tests with both expectations, every number the research note cites (summary.json), and SHA-256 checksums.+ - [Prediction registry](https://cybergenic.im/registry): Every prediction the engine locked before testing it, as a public md5 hash chain with downloadable preimages, an in-browser verifier and external anchors: OpenTimestamps proof (Bitcoin), Hugging Face (DOI 10.57967/hf/10762), figshare (DOI 10.6084/m9.figshare.34062204.v1).