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Claude Skills by bg-szy
github.com/bg-szy792 skills15 installs1,056 views
- Bio Pdb Structure Io Skills Structure IoParse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.Votes: 0GitHub stars: 6
- Bio Pdb Structure Modification Skills Structure ModificationModify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.Votes: 0GitHub stars: 6
- Bio Pdb Structure Navigation Skills Structure NavigationNavigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.Votes: 0GitHub stars: 6
- Bio Rnaseq Qc Skills Rnaseq QcRNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverage, and transcript integrity metrics. Use when validating RNA-seq libraries before differential expression analysis.Votes: 0GitHub stars: 6
- Bio Splicing Pipeline Skills Splicing PipelineEnd-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for complex events / heterogeneous cohorts, isoform-switching with NMD/ORF/domain consequences (IsoformSwitchAnalyzeR v2 + DRIMSeq+DEXSeq+stageR DTU), and sashimi visualizations. Use when performing comp...Votes: 0GitHub stars: 6
- Cbioportal DatabaseCancer genomics (TCGA et al.) via cBioPortal REST API. Retrieve somatic mutations, CNAs, expression, clinical data (survival/stage/treatment) across thousands of studies. Use for TMB, oncoprints, survival analysis. For population frequencies use gnomad-database; for drug-gene interactions use opentargets-database.Votes: 0GitHub stars: 6
- Deseq2 Differential ExpressionBulk RNA-seq DE with R/Bioconductor DESeq2. Negative binomial GLM, empirical Bayes shrinkage, Wald/LRT tests, multi-factor designs, Salmon tximeta import, apeglm LFC shrinkage, MA/volcano/heatmap viz. R gold standard. Use pydeseq2-differential-expression for Python; use edgeR for TMM normalization.Votes: 0GitHub stars: 6
- Hermes TweetInstall and operate Hermes Tweet, a Hermes Agent plugin for X/Twitter research, timeline reading, tweet analysis, and approval-gated private or state-changing operations. Use this skill when installing Hermes Tweet, researching X/Twitter accounts, monitoring launch signals, investigating mentions, auditing giveaways, or preparing gated X operations. Use proactively when a Hermes Agent workflow needs current X/Twitter context. Requires XQUIK_API_KEY for read and action tools.Votes: 0GitHub stars: 6
- MultipanelAssemble multiple plots into ONE publication-ready multi-panel journal figure (e.g. Figure 1 with panels A, B, C). Use whenever the user asks to combine, compose, or lay out several plots as a single composite figure — newly plotted from data or from already-rendered panels the user supplies (PNG/PDF). Ask the user to pick one of two approaches: (1) redraw every panel into one unified figure using independent, tightly packed `subfigures` (each sized to its own labels, so axes need NOT align),...Votes: 0GitHub stars: 6
- Nature FigureCreate, revise, audit, and export submission-grade scientific figures for Nature-family and other high-impact venues in Python (matplotlib/seaborn) or R (ggplot2/patchwork/ComplexHeatmap), including multi-panel plots, figures4papers-style work, and journal-ready SVG/PDF/TIFF outputs. Use for paper or scientific plots, manuscript data visualization, 论文配图、学术写作配图、科研绘图、科研作图、画图、作图、出图、论文图表、可视化. Define the conclusion, evidence logic, data integrity, template compatibility, export needs, and reviewer...Votes: 0GitHub stars: 6
- Nature PolishingPolish, restructure, or translate academic prose into concise Nature-leaning English while preserving facts, evidence boundaries, terminology, and citation intent. Use for manuscript paragraphs, abstracts, introductions, Results, discussions, conclusions, titles, Methods, Chinese drafts, proofreading, language editing, and general academic or scientific writing. Also use to shorten bloated Results, allocate evidence across main text, captions, and Supplementary Information, prevent reviewer-d...Votes: 0GitHub stars: 6
- Nature SharedInternal shared-reference support package for installed Nature Skills, including nature-writing, nature-polishing, nature-response, nature-reader, and nature-paper2ppt. Do not invoke it as a standalone user workflow. Load only the specific core or journal-format file requested by another Nature skill.Votes: 0GitHub stars: 6
- Nature WritingDraft, restructure, or plan Nature-style manuscript sections and initial-submission materials from author-provided claims, results, figures, notes, or Chinese drafts. Use for abstracts, introductions, related work, methods, Results or experiments, discussions, conclusions, titles, full manuscript arguments, and first-submission packages such as cover letters, title pages, highlights, author contributions, availability or declaration text, and reviewer suggestions. Also use to classify Results...Votes: 0GitHub stars: 6
- Omics PlottingPublication-style figure authoring for omics / bioinformatics results. Use whenever the user asks for a (single) plot, figure, or chart from analysis results or a data table — volcano, MA, expression / correlation heatmap, GSEA bar / dot plot, box / violin / bar / ridgeline, PCA / UMAP / t-SNE, Kaplan–Meier. The figures are drawn with matplotlib / seaborn; this skill supplies the shared style and copy-paste recipes so every figure looks like one consistent, journal-ready system. To combine se...Votes: 0GitHub stars: 6
- One Way DoorFlags irreversible decisions before commit. Use for data models, infra, auth boundaries, API contracts, event schemas, CI/CD.Votes: 0GitHub stars: 6
- Page MonitoringWeb page change detection, availability tracking, and RSS feed generation. Use to monitor changes, downtime, or make a feed.Votes: 0GitHub stars: 6
- Pdf DesignDesigns PDF reports and proposals from HTML with previews and branding. Use to create, export, or securely upload a PDF.Votes: 0GitHub stars: 6
- Project MemoryGenerates CLAUDE.md project memory files that transfer institutional knowledge. Use when setting up projects or onboarding.Votes: 0GitHub stars: 6
- Project RetrospectiveGenerates LESSONS.md files capturing institutional knowledge and failures. Use when closing out projects or investigations.Votes: 0GitHub stars: 6
- Prompt Engineering PatternsThis skill should be used when the user asks to \"optimize a prompt\", \"improve prompt performance\", \"design a prompt template\", \"write better prompts\", \"debug prompt issues\", \"use chain-of-thought\", \"structured prompting\", \"few-shot prompting\", or wants to apply advanced prompt engineering patterns for production LLM applications.Votes: 0GitHub stars: 6
- Protein Design Workflow"End-to-end guidance for protein design pipelines. Use this skill when: (1) Starting a new protein design project, (2) Need step-by-step workflow guidance, (3) Understanding the full design pipeline, (4) Planning compute resources and timelines, (5) Integrating multiple design tools.Votes: 0GitHub stars: 6
- Protein Qc"Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage filtering pipelines, (5) Computing PyRosetta interface metrics (dG, SC, dSASA), (6) Checking biophysical properties (instability, GRAVY, pI), (7) Ranking designs with composite ...Votes: 0GitHub stars: 6
- Proteinmpnn"Design protein sequences using ProteinMPNN inverse folding. Use this skill when: (1) Designing sequences for RFdiffusion backbones, (2) Redesigning existing protein sequences, (3) Fixing specific residues while designing others, (4) Optimizing sequences for expression or stability, (5) Multi-state or negative design.Votes: 0GitHub stars: 6
- Python Design PatternsPython design patterns including KISS, Separation of Concerns, Single Responsibility, and composition over inheritance. Use this skill when designing a new service or component from scratch and choosing how to layer responsibilities, when refactoring a God class or monolithic function that has grown too large, when deciding whether to add a new abstraction or live with duplication, when evaluating a pull request for structural issues like tight coupling or leaking internal types, when choosin...Votes: 0GitHub stars: 6
- Python PipelinePython data pipelines with modular architecture. Use for content workflows, batch jobs, or Google Sheets/Drive integration.Votes: 0GitHub stars: 6
- Rag ImplementationBuild Retrieval-Augmented Generation (RAG) systems for LLM applications with vector databases and semantic search. Use when implementing knowledge-grounded AI, building document Q&A systems, or integrating LLMs with external knowledge bases.Votes: 0GitHub stars: 6
- Rfdiffusion"Generate protein backbones using RFdiffusion, a diffusion-based generative model for de novo protein structure generation. Use this skill when: (1) Designing binder scaffolds for a target protein, (2) Generating novel protein backbones from scratch, (3) Scaffolding functional motifs into new proteins, (4) Specifying hotspot residues for interface design, (5) Creating symmetric oligomers.Votes: 0GitHub stars: 6
- Secure AuthSecure authentication patterns (OWASP, NIST). Use for login, registration, password reset, sessions, JWT, OAuth, MFA, passkeys.Votes: 0GitHub stars: 6
- Security ChecklistPre-deployment security audit organized by OWASP Top 10. Use when reviewing code before shipping or going to production.Votes: 0GitHub stars: 6
- SetupFirst-time setup for protein design tools. Use this skill when: (1) User is new and hasn't run any tools yet, (2) Commands fail with \"file not found\" or \"modal: command not found\", (3) Modal authentication errors occur, (4) User asks how to get started or set up the environment, (5) biomodals directory is missing or tools aren't working.Votes: 0GitHub stars: 6
- Social Media IntelligenceSocial media monitoring, narrative tracking, and OSINT. Use when tracking viral spread, coordinated campaigns, or account vetting.Votes: 0GitHub stars: 6
- Solublempnn"Solubility-optimized protein sequence design using SolubleMPNN. Use this skill when: (1) Designing for E. coli expression, (2) Optimizing solubility of designed proteins, (3) Reducing aggregation propensity, (4) Need high-yield expression, (5) Avoiding inclusion body formation.Votes: 0GitHub stars: 6
- Source VerificationVerify sources, claims, images, video, documents, interviews, and synthetic media with SIFT and a durable evidence trail. Use before relying on uncertain material.Votes: 0GitHub stars: 6
- 1passwordGuide for implementing 1Password secrets management - CLI operations, service accounts, Developer Environments, and Kubernetes integration. Use when retrieving secrets, managing vaults, configuring CI/CD pipelines, integrating with External Secrets Operator, managing Developer Environments, or automating secrets workflows with 1Password.Votes: 0GitHub stars: 6
- Alz AcceleratorDeploy Azure Landing Zones using the ALZ Accelerator with AVM (Azure Verified Modules). Use this skill whenever the user mentions Azure Landing Zones, ALZ, Azure landing zone accelerator, AVM modules for landing zones, deploying management groups, hub-and-spoke networking, Virtual WAN, platform landing zones, or asks about Bicep vs Terraform for Azure infrastructure. Also trigger when the user wants to bootstrap CI/CD for Azure platform deployment, set up management groups hierarchy, or deplo...Votes: 0GitHub stars: 6
- Argocd AdvancedAdvanced ArgoCD operations beyond the core CLI/API — multi-cluster ApplicationSet generators, automated image updates, new-cluster bootstrapping, and workload onboarding via templated ApplicationSets. USE WHEN working with ApplicationSet CRDs (list, cluster, git, matrix, merge, SCM, pull request, plugin generators), configuring ArgoCD Image Updater (semver/digest/newest-build update strategies + git write-back), bootstrapping a new Kubernetes cluster into a multi-repo GitOps setup, registerin...Votes: 0GitHub stars: 6
- ArgocdclusterbootstrappingComplete ArgoCD cluster bootstrapping skill for diagnosing sync failures, creating root Applications (app-of-apps), curating ApplicationSets via Kustomize, and resolving missing CRD dependencies. USE WHEN argocd bootstrap OR app-of-apps pattern OR root application OR applicationset gitops management OR argocd sync failed missing CRD OR kustomize applicationset curation OR argocd cluster onboarding.Votes: 0GitHub stars: 6
- ArgocdimageupdaterManage ArgoCD Image Updater configuration, drift resolution, and ImageUpdater CRDs. USE WHEN argocd image updater, image update drift, ImageUpdater CRD, extraObjects helm, environment-scoped image updates, argocd-image-updater troubleshooting.Votes: 0GitHub stars: 6
- AtuinShell history management with Atuin. Use when configuring shell history, setting up history sync, searching command history, importing history from other shells, troubleshooting atuin issues, or optimizing history workflows. Covers installation, sync setup, search modes, statistics, and self-hosting.Votes: 0GitHub stars: 6
- Az Aks AgentAzure AKS Agentic CLI - AI-powered troubleshooting and insights tool for Azure Kubernetes Service. Use when diagnosing AKS cluster issues, getting cluster health insights, troubleshooting networking/storage/security problems, or analyzing cluster configuration with natural language queries.Votes: 0GitHub stars: 6
- AztfexportUse when exporting existing Azure resources to Terraform using aztfexport. Triggers on aztfexport, Azure import to Terraform, export Azure resource, bring Azure under Terraform management, reverse-engineer Azure infrastructure, bootstrap IaC from live Azure resources. Covers resource, resource-group, and query modes.Votes: 0GitHub stars: 6
- Azure Ad SsoAzure AD OAuth2/OIDC SSO integration for Kubernetes applications. Use when implementing Single Sign-On, configuring Azure AD App Registrations, restricting access by groups, or integrating tools (DefectDojo, Grafana, ArgoCD, Harbor, SonarQube) with Azure AD authentication.Votes: 0GitHub stars: 6
- Azure Cost Management AppInstall and connect the Azure Cost Management App (by Microsoft Corporation) in Power BI Service via browser automation. Use this skill whenever the user mentions installing, deploying, connecting, or configuring the Azure Cost Management template app in Power BI, or when they want to connect Power BI to their EA (Enterprise Agreement) enrollment for cost visibility. Also triggers when the user says "connect your data" on the Cost Management App, wants to set up EA cost data in Power BI, or n...Votes: 0GitHub stars: 6
- Azure DevopsComprehensive Azure DevOps REST API skill for work items, pipelines, repos, test plans, wikis, and search operations via MCP tools and direct API callsVotes: 0GitHub stars: 6
- Azure FinopsAzure FinOps reservation analysis, cost validation, waste discovery, and executive reporting. USE WHEN user says 'validate costs', 'check reservations', 'find waste', 'orphaned resources', 'reservation coverage', 'savings analysis', 'draft response for', 'cost analysis', 'are these reservations', 'reservation gaps', OR any Azure cost optimization request.Votes: 0GitHub stars: 6
- Azure Landing Zone ChecklistFill out Microsoft Azure Landing Zone (ALZ) Accelerator checklists by interviewing the user, mapping their Azure subscriptions, integrating IP addressing documentation, and applying Microsoft Cloud Adoption Framework best practices. Produces a completed Excel checklist (.xlsx) ready for ALZ deployment. Use this skill whenever the user mentions Azure Landing Zone, ALZ checklist, landing zone accelerator, platform landing zone configuration, ALZ bootstrap, hub-and-spoke setup, Azure network top...Votes: 0GitHub stars: 6
- Azure Network CalculatorAzure network planning — CIDR calculation, subnet allocation, VNet sizing, IP address planning, snet layout, network capacity, Azure networking, hub-spoke topology. USE WHEN CIDR, subnet, VNet, snet, network planning, IP address, Azure networking, calculate network, plan network, validate CIDR, network capacity, address space.Votes: 0GitHub stars: 6
- Bmad OrchestrateParallel BMAD workflow orchestration using git worktrees and tmux. USE WHEN BMAD parallel, orchestrate sprint, run stories in parallel, worktree orchestration, sprint acceleration, parallel dev stories, bmad worktree, parallelize BMAD, accelerate epic.Votes: 0GitHub stars: 6
- Cloudflare DnsComprehensive guide for managing Cloudflare DNS with Azure integration. Use when configuring Cloudflare as authoritative DNS provider for Azure-hosted applications, managing DNS records via API, setting up API tokens, configuring proxy settings, troubleshooting DNS issues, implementing DNS security best practices, or integrating External-DNS with Cloudflare for Kubernetes workloads.Votes: 0GitHub stars: 6
- CommitStage, commit, and push changes to the current branch. Use when asked to commit, push, or create a commit for the current task.Votes: 0GitHub stars: 6