Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations.
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling, analyzing per-position read data, or calculating a — from…
Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux.
Align RNA-seq reads with HISAT2, a memory-efficient splice-aware aligner. Use when STAR's memory requirements are too high or for general RNA-seq alignment.
Gene Ontology over-representation analysis using clusterProfiler enrichGO. Use when identifying biological functions enriched in a gene list from differential expression — from…
Test Temporal workflows with pytest, time-skipping, and mocking strategies. Covers unit testing, integration testing, replay testing, and local development setup.
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for RNA velocity analysis.
Orchestrate Jira workflows end-to-end. Use when building stories with approvals, transitioning items through lifecycle states, or syncing task completion with Jira.
Statistical methods for calling hits in CRISPR screens. Covers MAGeCK, BAGEL2, drugZ, and custom approaches for identifying essential and resistance genes.
When the user wants to find information sources for content ideation, competitor monitoring, or industry tracking.
Automate Twitter/X with posting, engagement, and user management via inference.sh CLI. Apps: x/post-tweet, x/post-create (with media), x/post-like, x/post-retweet, x/dm-s — from…
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expressi — from…
Adjust communication style based on whether the user is in a relational (exploratory, hedging) or transactional (direct, technical) mode.
Evaluate systems through an entropy/negentropy lens — is this system decaying or growing? Use when making architecture decisions, evaluating system health, or when the user…
Walk through omicverse's single-cell preprocessing tutorials to QC PBMC3k data, normalise counts, detect HVGs, and run PCA/embedding pipelines on CPU, CPU–GPU mixed, or GPU stacks.
Use when you have a spec or requirements for a multi-step task, before touching code — from bg-szy/TOP-SKILLS
Enumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from building blocks using defined chemical reactions with…
Hardware-agnostic quantum ML framework with automatic differentiation. Use when training quantum circuits via gradients, building hybrid quantum-classical models, or need — from…
Quantifies biodiversity from species abundance/incidence tables using Hill numbers (iNEXT) with coverage-based rarefaction-extrapolation (Chao & Jost 2012), asymptotic richness…
Master C#/.NET backend development patterns for building robust APIs, MCP servers, and enterprise applications.
Execute git commit with conventional commit message analysis, intelligent staging, and message generation.
Manage issues, projects & team workflows in Linear. Use when the user wants to read, create or updates tickets in Linear. — from bg-szy/TOP-SKILLS
Authentication and access control skill for Next.js 15 + Supabase applications. Use when implementing user authentication, protecting routes, managing user sessions, enforcing…
Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies — from…
Create a concise plan. Use when a user explicitly asks for a plan related to a coding task. — from bg-szy/TOP-SKILLS
Visualize copy number profiles, segments, and compare across samples. Create publication-quality plots of CNV data from CNVkit, GATK, or other callers.
Extracts and assigns COSMIC v3.4 mutational signatures (84 SBS / 11 DBS / 18 ID / 24 CN / 16 SV) from somatic VCFs using SigProfilerSuite, MutationalPatterns, MuSiCal mvNMF,…
为 Datadata 平台编写 DQL 数据处理脚本 — 基于 Starlark 的扩展脚本语言，支持 DataFrame/Series 操作、SQL 查询、HTTP 请求等。当用户需要编写数据转换、数据清洗、数据生成或自定义数据处理逻辑时使用此 skill。
End-to-end Hi-C analysis workflow from contact pairs to compartments, TADs, and loops. Covers cooler matrices, cooltools analysis, and visualization.
Identify differentially bound regions across CLIP-seq conditions (knockdown vs control, treatment vs vehicle, disease vs healthy) using DEWSeq (sliding-window DESeq2), Flipper…
Convert content between platforms (blog to Twitter thread, article to LinkedIn post, etc.). Optimize for each platform's format, tone, and best practices.
Implement secure secrets management for CI/CD pipelines using Vault, AWS Secrets Manager, or native platform solutions.
Organizational coding standards and architectural patterns. References comprehensive skills for detailed patterns. Use when making architecture decisions or implementing features.
Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifying questions — from…
Opinionated backend development standards for Node.js + Express + TypeScript microservices. Covers layered architecture, BaseController pattern, dependency injection, Prisma…
Comprehensive backend development guide for Node.js/Express/TypeScript microservices. Use when creating routes, controllers, services, repositories, middleware, or workin — from…
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), library complexity, and IDR (Irreproducibility Discove — from…
Request and process code reviews with proper context. Use after completing significant implementation work.
Statistical models library for Python. Use when you need specific model classes (OLS, GLM, mixed models, ARIMA) with detailed diagnostics, residuals, and inference.
Comprehensive structural variant (SV) analysis skill for clinical genomics. Classifies SVs (deletions, duplications, inversions, translocations), assesses pathogenicity using…
CRISPResso2 for analyzing CRISPR gene editing outcomes. Quantifies indels, HDR efficiency, and generates comprehensive editing reports.
Retrieve records from NCBI databases using Biopython Bio.Entrez (EFetch, ESummary). Use when downloading sequences, fetching GenBank/GenPept records, getting document sum — from…
Combine vector and keyword search for improved retrieval. Use when implementing RAG systems, building search engines, or when neither approach alone provides sufficient r — from…
Vitest testing patterns and strategies for unit tests, agent tests, and API tests with Supabase mocking
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random — from…
Implement adaptive learning with ReasoningBank for pattern recognition, strategy optimization, and continuous improvement.
Publish Markdown articles to X (Twitter) Articles editor with proper formatting. Use when user wants to publish a Markdown file/URL to X Articles, or mentions "publish to — from…
Search PubMed and bioRxiv, summarise papers with LLM, build citation graphs, and generate literature review sections.
Senior Regulatory Affairs Manager expertise for HealthTech and MedTech companies. Provides strategic regulatory guidance, submission management, regulatory pathway analys — from…
Workflow from differential expression results to functional enrichment analysis. Covers GO, KEGG, Reactome enrichment with clusterProfiler and visualization.
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan.
Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences.
Creates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot.
Mobile game development principles. Touch input, battery, performance, app stores. — from bg-szy/TOP-SKILLS
Extract and analyze mutational signatures from somatic variants using SigProfiler or MutationalPatterns to characterize mutagenic processes.
Comprehensive fullstack development skill for building complete web applications with React, Next.js, Node.js, GraphQL, and PostgreSQL.
End-to-end gene regulatory network inference pipeline from processed single-cell data to regulon discovery and perturbation simulation.
Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation.
Generate AI images with FLUX, Gemini, Grok, Seedream, Reve and 50+ models via inference.sh CLI. Models: FLUX Dev LoRA, FLUX.2 Klein LoRA, Gemini 3 Pro Image, Grok Imagine — from…
Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity.