Skill Claude CodeCodex
Use for any task involving the tangermeme library — post-training analysis of genomic sequence-to-function (S2F) deep learning models. Triggers on predictions, DeepLIFT/SHAP attributions, marginalization/ablation/spacing of motifs, saturation mutagenesis (ISM), variant effect scoring, sequence design, seqlet calling…
Skill Claude CodeCodex
Use for any task involving the ledidi library — gradient-based design of minimal edits to categorical sequences (DNA/RNA/protein) so that a frozen oracle model predicts a desired output. Triggers on designing or editing a sequence, inserting or knocking out a motif or binding site, hitting a target model output, cell…
Instructions file
Instructions for jmschrei/cherimoya, covering cherimoya, layout, commands, conventions and gotchas (non-obvious).
Skill Claude CodeCodex
Train, evaluate, and use Cherimoya sequence-to-function genomic models with the cherimoya command-line tools or Python API. Use when a user wants to run the end-to-end pipeline, use a trained model to do downstream tasks, or troubleshoot a run. Designed for users who may be new to Cherimoya or to sequence modeling…