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Query the Cancer Dependency Map (DepMap) for gene dependency scores, drug sensitivity, and cancer-specific genetic vulnerabilities.
query_depmap.py for keyless data retrieval from Figshare.\n- References: Detailed mappings of DepMap data files (CRISPRGeneEffect, Model, etc.).\n- Instructions: Comprehensive Python workflows for loading matrices, finding selective dependencies, and biomarker analysis.\n\n## Compatible agents\nClaude Code, OpenClaw, and any LLM-based agent capable of executing Python for data analysis.This skill has not been reviewed by our automated audit pipeline yet.
Mixed Methods Research Design
Comprehensive guide for designing and integrating qualitative and quantitative research approaches using established academic frameworks.
AlterLab Deep Research
A 13-agent, PRISMA-capable research pipeline that runs scoping, systematic literature search, verification, synthesis, meta-analysis, and APA‑style reporting fo
ClinVar Database (AlterLab)
Search and interpret NCBI ClinVar variant data, access via E-utilities or FTP, annotate VCFs, and incorporate review-status and evidence best practices for geno
AlterLab PyMC — Bayesian Modeling
Bayesian modeling workflow using PyMC (v5+): build hierarchical models, run MCMC (NUTS) or variational inference, diagnose sampling, and compare models with LOO
bioRxiv Database Search
Search and retrieve life-sciences preprints from bioRxiv via API.
Academic Statistical Analysis
Guided hypothesis testing, assumption checking, and APA-formatted reporting.
GeoPandas Geospatial Analysis
Advanced spatial analysis for vector data including coordinate reprojection, spatial joins, and choropleth mapping using the GeoPandas library.
Seq Wrangler
Sequence data QC, trimming, alignment, and BAM processing pipeline helper — wraps FastQC, fastp/Trimmomatic, BWA/Bowtie2/Minimap2, and SAMtools for automated re
ToolUniverse Gateway
Unified agent gateway to 1000+ scientific tools (bioinformatics, drug discovery, genomics) via Harvard's ToolUniverse, returning JSON for downstream workflows.
MatchMS (mass spectrometry processing)
Mass spectrometry data processing: import/export mzML/MGF/MSP, filter and normalize spectra, compute spectral similarity (cosine/modified cosine), and build rep
Precision Oncology Treatment Advisor
Evidence-graded guidance to translate tumor molecular profiles into prioritized treatment options, resistance analysis, and clinical trial matches using curated
KEGG Pathway Enrichment (clusterProfiler)
Run KEGG pathway and module enrichment using clusterProfiler (enrichKEGG/enrichMKEGG) to find metabolic and signaling pathways over-represented in a gene list.
Network Toxicology & Docking Research Planner
Generates four-tier network toxicology + molecular docking study designs (Lite → Publication+) with step-by-step workflows, validation strategies, figure plans,
Bizard — Biomedical Visualization Atlas
A comprehensive atlas of biomedical data visualization tutorials and examples (R/Python/Julia) that provides reproducible code and guidance for plots used in bi
Bismark Methylation Calling
Extract per-cytosine methylation calls (CpG/CHG/CHH) from Bismark-aligned BAMs and produce bedGraph/coverage reports for downstream analysis.