Build RAG (Retrieval Augmented Generation) pipelines with web search and LLMs. Tools: Tavily Search, Exa Search, Exa Answer, Claude, GPT-4, Gemini via OpenRouter.
Test smart contracts comprehensively using Hardhat and Foundry with unit tests, integration tests, and mainnet forking.
Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT with reduced models, time as factor vs continuous vs natural…
Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer…
Use when starting any conversation - establishes mandatory workflows for finding and using skills, including using Read tool before announcing usage, following brainstorm — from…
Convert a finished raster image, especially a generated poster or visual resume, into an image-based PDF with an additional selectable, copyable, searchable text layer.
Map N6-methyladenosine (m6A) RNA modifications at single-nucleotide resolution using miCLIP (Linder 2015), miCLIP2 + m6Aboost machine learning (Kortel 2021), GLORI (Liu 2023,…
Test whether two or more traits share a causal variant at a locus using Bayesian colocalization (coloc.abf, coloc.susie, HyPrColoc, moloc, eCAVIAR, SMR/HEIDI, PWCoCo, SharePro).
Execute Python code in a safe sandboxed environment via [inference.sh](https://inference.sh). Pre-installed: NumPy, Pandas, Matplotlib, requests, BeautifulSoup, Selenium — from…
Use when executing implementation plans with independent tasks in the current session — from bg-szy/TOP-SKILLS
Conduct WCAG 2.2 accessibility audits with automated testing, manual verification, and remediation guidance.
Validate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics.
Query Ensembl genome database REST API for 250+ species. Gene lookups, sequence retrieval, variant analysis, comparative genomics, orthologs, VEP predictions, for genomic — from…
Spreadsheet toolkit (.xlsx/.csv). Create/edit with formulas/formatting, analyze data, visualization, recalculate formulas, for spreadsheet processing and analysis.
Infers dynamic gene regulatory networks from bulk time-series expression data using Granger causality (statsmodels), dynGENIE3 (Extra-Trees on ODE-derived expression derivatives),…
Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <-> CSR…
Reconcile gene trees against a species tree under probabilistic models of duplication, transfer, and loss (DTL) using ALE (Szöllősi 2013 amalgamated likelihood), GeneRax (Morel…
Download large datasets from NCBI efficiently using EPost, history server, batching, rate limiting, and retry logic.
Builds classification models for omics data using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs.
Four-phase root cause investigation before attempting fixes. Use when debugging bugs, test failures, or unexpected behavior.
End-to-end proteomics workflow from MaxQuant output to differential protein abundance. Orchestrates data import, normalization, imputation, and statistical testing with l — from…
Query UniProt's REST API (post-2022 endpoint at rest.uniprot.org) for protein sequences, annotations, GO terms, cross-references, ID mappings, and proteomes.
Smart dependency management for any language. Auto-detects project type, applies safe updates automatically, prompts for major versions, diagnoses and fixes dependency issues.
Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2.
When the user wants to optimize post-signup onboarding, user activation, first-run experience, or time-to-value.
Enforce RED-GREEN-REFACTOR cycle. Use when implementing features, fixing bugs, or writing any production code.
SwiftUI text styling and rich text editing patterns. Use when displaying styled text, building rich text editors, working with AttributedString, implementing TextEditor with…
Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization.
Complete browser automation with Playwright. Auto-detects dev servers, writes clean test scripts to /tmp.
Queries myvariant.info BioThings aggregator for ClinVar, gnomAD, dbSNP, dbNSFP, COSMIC, CADD, and CIViC annotations in batched, version-tracked requests.
Collaborative design exploration that refines ideas into validated specs through iterative questioning.
UI/UX design intelligence. 50 styles, 21 palettes, 50 font pairings, 20 charts, 9 stacks (React, Next.js, Vue, Svelte, SwiftUI, React Native, Flutter, Tailwind, shadcn/ui — from…
Python library for working with geospatial vector data including shapefiles, GeoJSON, and GeoPackage files.
Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data.
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers.
Visualize metagenomic profiles using R (phyloseq, microbiome) and Python (matplotlib, seaborn). Create stacked bar plots, heatmaps, PCA plots, and diversity analyses.
Modern shell prompt configuration with Powerlevel10k and Zsh Vi Mode. Use when configuring shell prompts, setting up vi/vim keybindings in zsh, customizing cursor styles per mode,…
Assembles a genome de novo from Illumina short reads with SPAdes (isolate/careful/sc/meta/plasmid/rna modes), MEGAHIT (low-memory, huge datasets), Unicycler (bacterial…
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado basecaller. Covers model selection, GPU acceleration, modified base detection, and qual — from…
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
Use when designing, architecting, or planning a new system from requirements or ideas - transforms concepts into navigable design catalog using EventStorming methodology, Mermaid…
When the user wants to create, optimize, or structure Terms of Service page. Also use when the user mentions "terms of service," "terms and conditions," "terms of use," "user…
Build scalable design systems with Tailwind CSS, design tokens, component libraries, and responsive patterns.
Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold,…
Automate Render tasks via Rube MCP (Composio): services, deployments, projects. Always search tools first for current schemas. — from bg-szy/TOP-SKILLS
Generate full songs and instrumental tracks with ElevenLabs Music on RunComfy via the `runcomfy` CLI.
Deep learning framework (PyTorch Lightning). Organize PyTorch code into LightningModules, configure Trainers for multi-GPU/TPU, implement data pipelines, callbacks, logging (W&B,…
Security review or audit of code, architecture, or infrastructure - Threat modeling sessions - Reviewing PRs for security implications
Create a PR for this branch. ALWAYS links related issues and uses closing keywords to auto-close them on merge.
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
Use when working on Nuxt 4+ projects - provides server routes, file-based routing, middleware patterns, Nuxt-specific composables, and configuration with latest docs.
JavaScript/TypeScript SDK for inference.sh - run AI apps, build agents, integrate 150+ models. Package: @inferencesh/sdk (npm install).
Use when encountering any bug, test failure, or unexpected behavior, before proposing fixes — from bg-szy/TOP-SKILLS
Configure timezone for Kubernetes pods using TZ environment variable. Use when deploying workloads that need Brazil/São Paulo timezone or when logs show UTC (+0000) instead of…
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
Tests genotype-environment associations and identifies adaptive loci while correcting for the four-confound landscape (structure, demography, background selection, sampling…
Implement data quality validation with Great Expectations, dbt tests, and data contracts. Use when building data quality pipelines, implementing validation rules, or esta — from…
Use when starting any conversation - establishes how to find and use skills, requiring Skill tool invocation before ANY response including clarifying questions — from…
When the user wants to promote via forums, communities, or invite users to join a community. Also use when the user mentions "forum promotion," "Indie Hacker," "Hacker News,"…
Analyzes disease patterns and health events through epidemiological lens using surveillance systems, — from bg-szy/TOP-SKILLS