Skill UI

Programmatic access to the COSMIC cancer mutation database for downloading mutations, Cancer Gene Census, mutational signatures, fusions, copy number, expression, and resistance data to fuel oncology research or bioinformatics pipelines after authentication.

Query and download the NCI Imaging Data Commons public cancer imaging datasets via idc-index, filter by metadata, fetch DICOM files, visualize series, and respect licensing details for AI training or research.

Access multi-dimensional cancer genomics data via cBioPortal REST API for mutation, copy-number, expression, and survival insights across TCGA/GENIE studies, enabling target validation and clinical association analyses programmatically with Python clients.

Access DepMap data to fetch CRISPR Chronos dependency scores, drug sensitivity readouts, and gene effect profiles for cancer cell lines, supporting target validation, biomarker discovery, and synthetic-lethality research via API or downloads.

This tool provides access to the Cancer Dependency Map (DepMap) data, derived from genome-wide CRISPR screens, RNAi, and compound sensitivity assays. It allows users to query gene dependency scores, identify cancer-specific vulnerabilities, predict synthetic lethal interactions, and validate potential oncology drug targets across various cancer cell lines.

Utilizes the idc-index package to query and download large-scale, public cancer imaging datasets from the NCI Imaging Data Commons. This skill allows users to select image subsets based on diverse metadata (e.g., cancer type, modality, anatomical site) and download raw DICOM files for advanced AI training, medical research, and visualization. No authentication is required for data access.

Provides comprehensive guidelines for statistical analysis and reporting in biological manuscripts, particularly in cancer research. It teaches researchers how to correctly define 'n' (distinguishing biological from technical replicates), select appropriate statistical tests (ANOVA, survival analysis, etc.), and manage multiple comparisons, ensuring high scientific rigor and reproducibility in published data.

A comprehensive guide for planning and auditing highly rigorous biological experimental protocols, particularly for cancer mechanism studies. It emphasizes orthogonal validation across independent systems (in vitro, in vivo, human), detailing requirements for controls, replicates, sample size justification, randomization, and blinding to ensure scientific rigor.

gget is a versatile CLI and Python package designed for rapid, reproducible bioinformatics searches across major genomic reference databases (e.g., Ensembl, UniProt). It allows users to quickly query gene metadata, perform initial BLAST/BLAT style alignments, and explore associated pathways, cancer, or disease modules. It is ideal for initial data exploration and generating reproducible evidence logs before building complex, full-scale local pipelines.