Git-bug issue tracker commands. Use when asked about managing issues, creating bugs, or using the issue tracker.

Attach images to GitHub PRs and issues via a scratch repo

Imported skill github_utils from openai

Manages GitLab commits. Use for listing, creating, reverting, or querying commit details/diffs/comments. Triggers: commit history, changes, reversions.

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Comprehensive skill for interacting with Grafana's HTTP API to manage dashboards, data sources, folders, alerting, annotations, users, teams, and organizations. Use when Claude needs to (1) Create, read, update, or delete Grafana dashboards, (2) Manage data sources and connections, (3) Configure alerting rules, contact points, and notification policies, (4) Work with folders and permissions, (5) Manage users, teams, and service accounts, (6) Create or query annotations, (7) Execute queries against data sources, or any other Grafana automation task via API.

Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression and omics data visualization. Use when visualizing expression patterns across samples or identifying co-expressed gene clusters.

Imported skill history from langchain

Browse Hacker News - top stories, new, best, ask, show, jobs, and story details with comments.

Imported skill __init__ from langchain

A workflow for writing code comments concurrently with development to ensure accuracy and reduce rework. Use when actively coding, planning development tasks, or addressing code maintainability in ongoing software projects.

Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training classifiers or validating automated phenotyping results.

Create relationships between issues via comment references

Work with GitHub issues - create, list, update, comment, and search issues using gh CLI

1. Fetch issue details:

Queries JGI Lakehouse (Dremio) for genomics metadata from GOLD, IMG, Mycocosm, Phytozome. Downloads genome files from JGI filesystem using IMG taxon OIDs. Use when working with JGI data, GOLD projects, IMG annotations, or downloading microbial genomes.

Kotlin DSL - type-safe builders, Gradle DSL, @DslMarker

Comprehensive guide for Label Studio setup and usage on local server for data labeling and annotation.

Rust documentation practices for HASH codebase. Use when writing doc comments, documenting functions/types/traits/modules, creating error sections, using intra-doc links, following rustdoc conventions, or exploring crate APIs with cargo doc.

Tool and function calling patterns with LangChain4j. Define tools, handle function calls, and integrate with LLM agents. Use when building agentic applications that interact with tools.

Skill for creating and editing Spatie Laravel Data classes following Prowi conventions. Use when working with Data classes, DTOs, or data transfer objects. Enforces proper constructor-based properties, annotation-based validation, and Collection usage.

Fix last few build errors aggressively, get clean build, commit everything, and prepare for ship in Leavn iOS app

Manage project planning for the `libgraphql` workspace via `plans.md` files and code TODO comments.

Use when implementing Lightning address functionality - provides complete patterns for resolving Lightning addresses to invoices, generating invoices from addresses, displaying Lightning addresses in UI, and integrating with QR codes

Query, create, and manage Linear issues from the command line. Use when checking assigned work, viewing issue details, creating new issues, or updating issue status.

Comprehensive workflow for managing Linear issues using the linearis CLI tool. Handles issue creation, status tracking, commenting, and file downloads with clear decision trees for when to ask for approval vs. acting autonomously.

Use when working with Linear issues across development workflow - uses Linearis CLI with JSON output for zero-context issue management. Get details, create issues, update status, and add comments without consuming tokens in main session.

Linear issue-tracked development workflow. Auto-activates when starting work on issues, creating branches, changing status, writing comments, or creating PRs.

linkedin-content-strategy

Imported skill list_skills from openai

Builds real-time collaborative features with Liveblocks including presence, cursors, storage, comments, and notifications. Use when adding multiplayer experiences, collaborative editing, or live cursors to React applications.

Imported skill loading from langchain

This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling large-scale biological datasets. Use when tasks involve AnnData objects, h5ad files, single-cell RNA-seq data, or integration with scanpy/scverse tools.

Single-cell RNA-seq analysis. Load .h5ad/10X data, QC, normalization, PCA/UMAP/t-SNE, Leiden clustering, marker genes, cell type annotation, trajectory, for scRNA-seq analysis.

This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential expression, cell type annotation, multimodal integration, and spatial analysis tasks.

Manage Todoist tasks, projects, labels, filters, sections, comments, reminders, and workspaces via the `td` CLI. Use when the user wants to view, create, update, complete, or organize Todoist items, or mentions tasks, inbox, today, upcoming, projects, labels, or filters.

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Guide to annotating cell types in single-cell RNA-seq data. Covers manual marker-based, automated (CellTypist, scAnnotate), and reference-based (scArches, Azimuth, SingleR) approaches with decision framework for tool selection. Includes key marker genes for blood/immune, epithelial, and stromal lineages, validation checklist, and common pitfalls. Cross-references: scanpy-scrna-seq for preprocessing, celltypist-cell-annotation for automated classification, scvi-tools-single-cell for deep-learning-based label transfer.

Query PharmGKB (Clinical Pharmacogenomics) database via REST API for drug-gene interactions, clinical annotations, dosing guidelines (CPIC, DPWG), variant-drug associations, and pharmacogenomic pathways. Search by gene, drug, rsID, or pathway. No authentication required. For somatic cancer pharmacogenomics use cosmic-database or opentargets-database; for drug structures use chembl-database-bioactivity.

Query COSMIC (Catalogue Of Somatic Mutations In Cancer) for cancer somatic mutations, gene census data, mutational signatures, drug resistance variants, and cancer gene annotations. REST API v3.1 supports gene/sample/variant queries. Free registration required. For germline clinical variants use clinvar-database; for drug-target data use opentargets-database or chembl-database-bioactivity.

Query NCBI dbSNP for SNP records by rsID, gene, or genomic region via E-utilities (esearch, efetch, epost) and NCBI Variation Services REST API. Retrieve allele data, minor allele frequency, variant class (SNV, indel, MNV), clinical significance links, and cross-database IDs (ClinVar, dbVar, 1000G). Free access; 3 req/sec without API key, 10 req/sec with key. For clinical pathogenicity classifications use clinvar-database; for population frequencies use gnomad-database.

Counts aligned RNA-seq reads overlapping gene features in a GTF annotation. Takes sorted BAM files from STAR alignment and a GTF file; outputs a tab-delimited count matrix per gene across all samples. Handles strandedness (0=unstranded, 1=stranded, 2=reverse-stranded), paired-end, and multi-sample batch counting in a single command. Use Salmon instead for alignment-free quantification; use featureCounts when STAR BAMs already exist and a gene-level count matrix is needed.

Query NCBI Gene Expression Omnibus (GEO) for gene expression datasets and sample metadata via GEOparse Python library and E-utilities. Search datasets by keyword/organism/platform, download GSE series matrices, parse GPL platform annotations, extract GSM sample metadata, and load expression matrices into pandas. For single-cell data use cellxgene-census; for programmatic multi-DB access use gget-genomic-databases.

De novo motif discovery and known TF motif enrichment in ChIP-seq and ATAC-seq peak sets using HOMER. findMotifsGenome.pl searches for over-represented sequence patterns against a background; annotatePeaks.pl assigns genomic context (TSS distance, gene, repeat). Use after MACS3 peak calling to identify which transcription factors are enriched in your peaks, annotate peaks with nearest genes, and validate ChIP-seq quality by checking the target TF's own motif.

Calls narrow and broad peaks from ChIP-seq and ATAC-seq BAM files using a Poisson model. MACS3 callpeak identifies enriched genomic regions (transcription factor binding sites or histone marks) against an input/IgG control; outputs BED narrowPeak/broadPeak files for downstream motif analysis, annotation, and differential binding. Use narrow peaks for TF ChIP-seq and ATAC-seq; use broad peaks for H3K27me3, H3K9me3, and other broad histone marks.

Retrieve quantitative phenotype measurements across inbred mouse strains from the Mouse Phenome Database (MPD) for metabolic, behavioral, and physiological traits. Query strain means and raw individual measurements for body weight, glucose, blood pressure, behavioral assays, and 40+ additional procedures. Use for QTL analysis support, cross-strain phenotype comparison, and identifying mouse models for metabolic or behavioral traits. For mouse gene-disease-phenotype associations use monarch-database; for mouse genome annotations use ensembl-database.