tools-only/X-Skills - Page 40

cli

Slidev command-line interface reference

exporting

Export presentations to PDF, PPTX, PNG, or Markdown

hosting

Build and deploy Slidev presentations

stitch

Google Stitch design platform skill bundle. Covers design system extraction, prompt enhancement, iterative site building, React component conversion, Remotion walkthrough videos, and shadcn/ui component integration. Activate when user mentions Stitch,…

term-cli

Controls interactive terminal sessions for running long-lived processes, servers, REPLs, debuggers, and TUI programs without blocking. Use when you need to run dev servers (npm run dev), debuggers (pdb, gdb), REPLs (python, node), databases (psql, mysql), SSH…

second-opinion

Runs external LLM code reviews (OpenAI Codex or Google Gemini CLI) on uncommitted changes, branch diffs, or specific commits. Use when the user asks for a second opinion, external review, codex review, gemini review, or mentions /second-opinion.

gmail

Interact with Gmail - search emails, read messages, send emails, create drafts, and manage labels. Use when user asks to: search email, read email, send email, create email draft, mark as read, archive email, star email, or manage Gmail labels. Lightweight…

google-chat

Interact with Google Chat - list spaces, send messages, read conversations, and manage DMs. Use when user asks to: send a message on Google Chat, read chat messages, list chat spaces, find a chat room, send a DM, or create a new chat space. Lightweight…

sf-ai-agentscript

Agent Script DSL development skill for Salesforce Agentforce. Enables writing deterministic agents in a single .agent file with FSM architecture, instruction resolution, and hybrid reasoning. Covers syntax, debugging, testing, and CLI deployment.

hive-create

Step-by-step guide for building goal-driven agents. Creates package structure, defines goals, adds nodes, connects edges, and finalizes agent class. Use when actively building an agent.

hive

Complete workflow for building, implementing, and testing goal-driven agents. Orchestrates hive-* skills. Use when starting a new agent project, unsure which skill to use, or need end-to-end guidance.

swarm-task-planner

Creates dependency-based task plans for parallel AI agent execution. Transforms architecture docs and PRDs into priority-ordered tasks with acceptance criteria, sync checkpoints, and quality gates. Uses CLEAR+CoVe task design standards.

linting-root-cause-resolver

Resolve linting/type errors by investigating root causes, not silencing symptoms. Use when ruff, mypy, pyright, or basedpyright report issues. Researches rules, reads code context, loads python3-development skill, and elegantly rewrites code to fix underlying…

bio-gene-regulatory-networks-coexpression-networks

Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes using WGCNA and CEMiTool. Detects hub genes and module-trait relationships from bulk or single-cell expression data. Use when finding…

bio-workflows-grn-pipeline

End-to-end gene regulatory network inference pipeline from processed single-cell data to regulon discovery and perturbation simulation. Supports RNA-only (pySCENIC) and multiome (SCENIC+) paths. Use when building gene regulatory networks from single-cell…

bio-workflows-genome-annotation-pipeline

End-to-end genome annotation pipeline from assembled contigs to functional annotation, covering repeat masking, gene prediction, and functional assignment for both prokaryotic and eukaryotic genomes. Use when annotating a newly assembled genome from scratch.

bio-gene-regulatory-networks-differential-networks

Compare gene regulatory and co-expression networks between biological conditions to identify rewired regulatory relationships using DiffCorr. Detects gained, lost, and reversed gene-gene correlations between conditions. Use when comparing co-expression…

bio-gene-regulatory-networks-multiomics-grn

Build enhancer-driven gene regulatory networks by integrating single-cell RNA-seq and ATAC-seq data using SCENIC+ to identify eRegulons linking transcription factors to enhancers and target genes. Use when analyzing 10x multiome or paired scRNA+scATAC data to…

annotating-task-lineage

Annotate Airflow tasks with data lineage using inlets and outlets. Use when the user wants to add lineage metadata to tasks, specify input/output datasets, or enable lineage tracking for operators without built-in OpenLineage extraction.

bio-interaction-databases

Query protein-protein and gene interaction databases including STRING, BioGRID, and IntAct via their REST APIs and Python clients. Retrieve interaction networks, confidence scores, and functional enrichment. Use when building protein interaction networks,…

bio-rna-structure-structure-probing

Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucleotide reactivity profiles that constrain structure prediction. Use when processing SHAPE-MaP or DMS-MaPseq…

bio-gene-regulatory-networks-perturbation-simulation

Simulate transcription factor perturbation effects on cell state using CellOracle, which integrates GRN inference with in silico knockout and overexpression modeling. Predicts cell identity shifts and differentiation trajectory changes from TF perturbations.…

bio-genome-annotation-annotation-transfer

Transfer gene annotations between genome assemblies using Liftoff for same-species annotation liftover and MiniProt for cross-species protein-to-genome alignment. Enables rapid annotation of new assemblies using existing reference annotations. Use when…

bio-genome-annotation-functional-annotation

Assign GO terms, KEGG orthologs, Pfam domains, and EC numbers to predicted proteins using eggNOG-mapper and InterProScan. Produces functional summaries for downstream pathway and enrichment analysis. Use when adding functional annotation to predicted genes or…

bio-gene-regulatory-networks-scenic-regulons

Infer gene regulatory networks and identify transcription factor regulons from single-cell RNA-seq data using pySCENIC. Discovers co-expression modules with GRNBoost2, prunes by cis-regulatory motif enrichment, and scores regulon activity per cell with…

bio-data-visualization-network-visualization

Visualize biological networks including gene regulatory networks, protein interaction networks, and co-expression modules using NetworkX, PyVis, and Cytoscape automation. Produces interactive and publication-quality network figures. Use when creating network…

bio-copy-number-cnvkit-analysis

Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use when detecting CNVs from WES or targeted panel sequencing data.

bio-genome-annotation-eukaryotic-gene-prediction

Predict protein-coding genes in eukaryotic genomes using BRAKER3 for combined RNA-seq and protein evidence, or GALBA for protein-only evidence. Runs Augustus with trained parameters for accurate gene models. Use when annotating a newly assembled eukaryotic…

bio-rna-structure-secondary-structure-prediction

Predicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAfold, RNAalifold, RNAcofold). Computes base-pair probabilities, centroid structures, and consensus structures from alignments. Use when…

bio-genome-annotation-prokaryotic-annotation

Annotate bacterial and archaeal genomes with Bakta for comprehensive structural and functional annotation, or Prokka for lightweight annotation. Generates GFF3, GenBank, and FASTA outputs with NCBI-compatible locus tags. Use when annotating a newly assembled…

bio-causal-genomics-pleiotropy-detection

Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting…

authoring-dags

Workflow and best practices for writing Apache Airflow DAGs. Use when the user wants to create a new DAG, write pipeline code, or asks about DAG patterns and conventions. For testing and debugging DAGs, see the testing-dags skill.

bio-rna-structure-ncrna-search

Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rfam database. Identifies structured RNAs by sequence and secondary structure conservation. Use when querying sequences against Rfam,…

bio-genome-annotation-ncrna-annotation

Identify non-coding RNAs including tRNAs, rRNAs, snoRNAs, and regulatory RNAs using Infernal covariance model searches against Rfam and tRNAscan-SE for tRNA prediction. Use when performing genome-wide ncRNA annotation with assembly input producing GFF output.

bio-genome-annotation-repeat-annotation

Identify and classify repetitive elements and transposable elements using RepeatModeler for de novo repeat library construction and RepeatMasker for genome-wide repeat annotation. Quantify TE expression from RNA-seq with TEtranscripts. Use when masking…

docs-writer

Repo-aware documentation writer and maintainer for azure-agentic-infraops. Understands the full agent/skill architecture, scenario structure, naming conventions, and template system. Use when asked to "update the docs", "add documentation for a new…

bicep-code

Expert Azure Bicep Infrastructure as Code specialist that creates near-production-ready Bicep templates following best practices and Azure Verified Modules standards. Validates, tests, and ensures code quality.

diagnose

Interactive diagnostic agent that guides users through Azure resource health assessment, issue identification, and remediation planning. Uses approval-first execution for safety, analyzes single resources, and saves reports to agent-output/{project}/.

requirements

Researches and captures Azure infrastructure project requirements

bicep-plan

Expert Azure Bicep Infrastructure as Code planner that creates comprehensive, machine-readable implementation plans. Consults Microsoft documentation, evaluates Azure Verified Modules, and designs complete infrastructure solutions with architecture diagrams.