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DNAnexus Integration

dnanexus-integration

K-Dense-AI/scientific-agent-skills

Build and operate reproducible genomics workloads on DNAnexus using dx CLI, dxpy, apps/applets, native workflows, and Nextflow. Supports data transfers, app development, execution monitoring, and project automation for genomic data analysis pipelines.

gget Bioinformatics Query Tool

K-Dense-AI/scientific-agent-skills

Unified CLI and Python interface to 20+ bioinformatics databases for gene info, BLAST/BLAT, viral sequences, AlphaFold structures, enrichment, disease and expression queries.

Gtars Genomic Interval Toolkit

K-Dense-AI/scientific-agent-skills

Gtars offers local genomic interval models, set algebra, overlap/count operations, consensus and coverage, tokenization, fragment processing, and refget/BEDbase planning across Python, Rust, and CLI.

OMERO Microscopy Data Integration

omero-integration

K-Dense-AI/scientific-agent-skills

Securely inspect and automate microscopy data workflows against OMERO.server using omero-py, BlitzGateway, CLI, tables, annotations, ROIs, rendering, and documented APIs. Support scoped inventory, metadata export, and reviewed write operations.

Scanpy Single-Cell Analysis Pipeline

K-Dense-AI/scientific-agent-skills

Scanpy is a scalable Python toolkit for single-cell RNA-seq analysis, covering quality control, normalization, dimensionality reduction, clustering, and visualization. It supports converting R formats to h5ad and includes ready-to-run CLI scripts for end-to-end workflows, making it ideal for exploratory scRNA-seq analysis and publication-quality plotting.

Optimize ClickHouse Cloud Costs

clickhouse-cost-tuning

jeremylongshore/claude-code-plugins-plus-skills

A comprehensive guide to reducing expenses on ClickHouse Cloud. Learn advanced techniques for storage optimization (compression, TTL), compute resource tuning (scaling, thread limits), and query efficiency improvements. Use this when managing data budgets or analyzing high ClickHouse billing charges.

Collect ClickHouse Diagnostic Bundle

clickhouse-debug-bundle

jeremylongshore/claude-code-plugins-plus-skills

This tool collects comprehensive diagnostic data from ClickHouse system tables. It gathers crucial metrics, query logs, merge statuses, and disk usage information. It is essential for troubleshooting performance bottlenecks, preparing detailed support tickets, or investigating complex database infrastructure issues.

ClickHouse Concurrency And Resource Management

clickhouse-rate-limits

jeremylongshore/claude-code-plugins-plus-skills

This guide details how to configure and manage resource constraints in ClickHouse, addressing server-side limits, user quotas, and connection management. Use it when encountering "too many simultaneous queries," optimizing resource usage, or implementing robust rate limiting strategies in applications connecting to ClickHouse. Covers SQL quota setup and client-side pooling techniques.

ClickHouse Data Ingestion Pipelines

clickhouse-webhooks-events

jeremylongshore/claude-code-plugins-plus-skills

A comprehensive guide and implementation template for building robust data ingestion pipelines into ClickHouse. Supports multiple sources including HTTP webhooks (with batching), Kafka streams, S3, and direct SQL inserts. Demonstrates best practices for data handling, such as deduplication using ReplacingMergeTree and monitoring query logs, ensuring reliable, scalable data analytics.

Debugging Common ClickHouse Database Errors

clickhouse-common-errors

jeremylongshore/claude-code-plugins-plus-skills

This guide provides a quick reference for diagnosing and fixing the top common errors encountered in ClickHouse, including syntax errors, memory limit issues, write permission failures, and data type mismatches. It offers specific error codes, root causes, and actionable SQL solutions for smooth database operation and complex analytics.

ClickHouse Data Analysis and Querying

clickhouse-core-workflow-b

jeremylongshore/claude-code-plugins-plus-skills

This comprehensive guide provides advanced workflows for interacting with ClickHouse. It covers efficient bulk data insertion (CSV, JSON), complex analytical querying (funnel analysis, retention), implementing materialized views for pre-aggregation, and utilizing powerful window functions. Ideal for building high-performance OLAP dashboards and executing large-scale data transformations.

ClickHouse Quick Start and Data Analysis

clickhouse-hello-world

jeremylongshore/claude-code-plugins-plus-skills

This comprehensive guide teaches users how to set up a ClickHouse database environment. It covers creating a MergeTree table, inserting structured event data using TypeScript, and executing essential analytical queries (e.g., counting, grouping, unique user metrics). Ideal for beginners learning OLAP databases, testing connections, or mastering core data warehousing concepts.

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