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…
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