zamushwani/biomedical-ai-skills
Skill Claude CodeCodex
Joint analysis of two or more molecular layers on the same samples. Covers method selection, the preprocessing that decides whether integration works at all, MOFA+ factor analysis, similarity network fusion, joint clustering for cancer subtyping, supervised integration, and survival models built on integrated features.
zamushwani/biomedical-ai-skills
Skill Claude CodeCodex
Genomic predictors of radiation response: DNA damage repair pathway profiling, the Radiosensitivity Index and the Genomic-Adjusted Radiation Dose built on it, post-irradiation immune activation signatures, and an honest account of what the abscopal effect can and cannot be predicted from.
zamushwani/biomedical-ai-skills
Skill Claude CodeCodex
Full single-cell RNA-seq pipeline from raw counts to biological interpretation. Covers QC, normalization, batch integration, clustering, annotation, pseudobulk DE, trajectory inference, cell-cell communication, and TF activity. Dual-language: Seurat v5 (R) and scanpy (Python).
zamushwani/biomedical-ai-skills
Skill Claude CodeCodex
Processing and analysis of spatially resolved transcriptomics across sequencing-based (Visium, Visium HD, Slide-seq, Stereo-seq) and imaging-based (Xenium, MERSCOPE, CosMx) platforms. Covers loading, QC, normalization, and spatially variable gene detection. Dual-language: Python (squidpy/SpatialData) and R…
zamushwani/biomedical-ai-skills
Skill Claude CodeCodex
Time-to-event analysis for cancer clinical data. Covers Kaplan-Meier, Cox proportional hazards, competing risks, restricted mean survival time, and optimal cutpoint selection using the survival, ggsurvfit, tidycmprsk, and survRM2 packages.
zamushwani/biomedical-ai-skills
Skill Claude CodeCodex
Annotation and clinical interpretation of DNA variants in cancer. Covers VCF normalization and filtering, functional annotation with VEP, germline classification under ACMG/AMP, somatic classification under the AMP/ASCO/CAP tiers and the ClinGen/CGC/VICC oncogenicity standard, tumor mutational burden, microsatellite…