medchem

More from eturkes/claude-scientific-skills

• get-available-resources

  This skill should be used at the start of any computationally intensive scientific task to detect and report available system resources (CPU cores, GPUs, memory, disk space). It creates a JSON file with resource information and strategic recommendations that inform computational approach decisions such as whether to use parallel processing (joblib, multiprocessing), out-of-core computing (Dask, Zarr), GPU acceleration (PyTorch, JAX), or memory-efficient strategies. Use this skill before running analyses, training models, processing large datasets, or any task where resource constraints matter.

  8

• statistical-analysis

  Guided statistical analysis with test selection and reporting. Use when you need help choosing appropriate tests for your data, assumption checking, power analysis, and APA-formatted results. Best for academic research reporting, test selection guidance. For implementing specific models programmatically use statsmodels.

  8

• pytdc

  Therapeutics Data Commons. AI-ready drug discovery datasets (ADME, toxicity, DTI), benchmarks, scaffold splits, molecular oracles, for therapeutic ML and pharmacological prediction.

  7

• pydeseq2

  Differential gene expression analysis (Python DESeq2). Identify DE genes from bulk RNA-seq counts, Wald tests, FDR correction, volcano/MA plots, for RNA-seq analysis.

  7

• hypothesis-generation

  Structured hypothesis formulation from observations. Use when you have experimental observations or data and need to formulate testable hypotheses with predictions, propose mechanisms, and design experiments to test them. Follows scientific method framework. For open-ended ideation use scientific-brainstorming; for automated LLM-driven hypothesis testing on datasets use hypogenic.

  7

• phylogenetics

  Build and analyze phylogenetic trees using MAFFT (multiple alignment), IQ-TREE 2 (maximum likelihood), and FastTree (fast NJ/ML). Visualize with ETE3 or FigTree. For evolutionary analysis, microbial genomics, viral phylodynamics, protein family analysis, and molecular clock studies.

  7