Research skills

Browse reusable Agent Skills, each with a clear purpose and practical guidance.

dual-disease-transcriptomic-ml-planner

Generates complete dual-disease transcriptomic + machine learning research designs from a user-provided disease pair. Use when users want to identify shared DEGs, common hub genes, cross-disease biomarkers, or shared molecular mechanisms between two diseases using public GEO data. Triggers:"shared biomarker study for two diseases", "dual-disease transcriptomic ML paper", "identify common DEGs between disease A and B", "cross-disease hub gene discovery", "shared DEG + PPI + ROC design", "immune infiltration shared biomarker", or "I want to study disease X and Y together". Always outputs four workload configurations (Lite / Standard / Advanced / Publication+) with a recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, and publication upgrade path.

1.45k repo starsObserved in 2 repos
Research
GitHub

emerging-topic-scout

A real-time monitoring system for identifying "incubation period" research hotspots in biological and medical sciences before they are defined by mainstream journals.

1.45k repo starsObserved in 2 repos
Research
GitHub

ena-database

Access the European Nucleotide Archive (ENA) via REST APIs and FTP/Aspera to search and retrieve sequences, raw reads (FASTQ), assemblies, and metadata when you have accession IDs or need metadata-driven discovery for genomics pipelines.

1.45k repo starsObserved in 2 repos
Research
GitHub

encode-api

Access the ENCODE Project REST API to search for and retrieve biological data (biosamples, experiments, etc.). Use this skill when the user needs to query ENCODE data, search by keywords, or retrieve specific objects by accession ID.

1.45k repo starsObserved in 2 repos
Research
GitHub

encori-api

Access ENCORI (StarBase) database for miRNA-target, RNA-RNA, and other regulatory data. Invoke when user asks to search ENCORI or retrieve regulatory interactions.

1.45k repo starsObserved in 2 repos
Research
GitHub

etetoolkit

ETE (Environment for Tree Exploration) toolkit for phylogenetic and hierarchical tree analysis; use it when you need to parse/manipulate Newick/NHX trees, detect duplication/speciation events, integrate NCBI taxonomy, and render publication-quality figures.

1.45k repo starsObserved in 2 repos
Research
GitHub

evidence-level-ranker

Ranks papers by evidence family, methodological quality tier, validation depth, and claim discipline; assigns anchor, context-setting, mechanistic support, or caution citation roles; prevents prestige-based or design-label-based ranking errors.

1.45k repo starsObserved in 2 repos
Research
GitHub

faers-multi-drug-soc-planner

Generates complete FAERS-based multi-drug single-SOC safety comparison research designs from a user-provided drug set, comparator, and adverse event domain. Always use this skill when users want to compare safety signals across multiple drugs using FAERS or OpenFDA data within one System Organ Class (SOC) or bounded AE domain. Trigger for:"FAERS study comparing drugs within one SOC", "publishable FAERS safety comparison paper", "compare neuropsychiatric adverse events across beta-blockers", "Lite/Standard/Advanced FAERS safety plans", "active-comparator restricted disproportionality", "adjusted ROR logistic regression FAERS", "within-class head-to-head drug comparison", "pharmacovigilance signal comparison", "single-SOC PT-level FAERS design", or any phrasing like "I want to compare drug X and drug Y for adverse events in FAERS" or "build a comparative pharmacovigilance paper". Always output four workload configurations (Lite / Standard / Advanced / Publication+) with a recommended primary plan, step-by-step workflow, figure plan, validation strategy, minimal executable version, and publication upgrade path.

1.45k repo starsObserved in 2 repos
Research
GitHub

faers-pharmacovigilance-disproportionality-research-planner

Generates complete FAERS-style pharmacovigilance disproportionality research designs from a user-provided drug class, comparator strategy, adverse-event domain, and patient-group stratification. Always use this skill whenever a user wants to design, plan, or build a spontaneous-report safety signal study using FAERS or a similar pharmacovigilance database, especially when the article logic includes product selection, indication-group stratification, MedDRA-based adverse-event extraction, serious-case filtering, suspect-drug and concomitant-exclusion logic, reporting odds ratio analysis, comparator-drug benchmarking, cross-drug comparison, and cautious signal interpretation without causal overclaiming. Covers five study patterns (single-drug disproportionality workflow, multi-drug class comparison workflow, indication-stratified workflow, comparator-controlled signal screening workflow...

1.45k repo starsObserved in 2 repos
Research
GitHub